Loading ...
Sorry, an error occurred while loading the content.

Atoms distance in a molecular dynamics

Expand Messages
  • Jeanne Cambefort
    Hello, I m new on CNS. I would like to generate N structures during a molecular dynamics. I employed model_anneal.inp downloaded on
    Message 1 of 6 , May 16, 2012
    View Source
    • 0 Attachment
      Hello,

      I'm new on CNS. 
      I would like to generate N structures during a molecular dynamics.
      I employed model_anneal.inp downloaded on http://cns.csb.yale.edu/v1.3/,
      with the following parameters : 
      - no .def file
      {===>} atom_select=(known);
      {===>} atom_fixed=(none);
      {===>} atom_harm=(none);
      {===>} md_type="cartesian";
      {===>} md_scheme="constant";
      {===>} temperature=300;
      {===>} tcontrol="coupling";

      The model_anneal.inp script makes a molecular dynamics well, but it 
      generates N structures only after the end of the molecular dynamics. Why ?
      I would like to order my resulted structures by time with measures.
      Please, how could I transform the model_anneal.inp to produce structures 
      during the molecular dynamics?
      I hope to be clear, I thank you very much for your help.

      Jeanne Cambefort
      Engineer in Bioinformatics
      Innovation Moléculaire et Thérapeutiques (IMT)
      Université François Rabelais
      UFR de Sciences Pharmaceutiques
      Parc Grandmont, Avenue Monge
      37200 Tours - France
      Tel : 33 (0)2 47 36 74 72



    • Ed Pozharski
      ... if you didn t touch traj_freq, it should... post the log-file, there might be a clue there. -- Oh, suddenly throwing a giraffe into a volcano to make water
      Message 2 of 6 , May 16, 2012
      View Source
      • 0 Attachment
        On Wed, 2012-05-16 at 16:25 +0200, Jeanne Cambefort wrote:
        > Please, how could I transform the model_anneal.inp to produce
        > structures during the molecular dynamics?

        if you didn't touch traj_freq, it should... post the log-file, there
        might be a clue there.



        --
        Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
        Julian, King of Lemurs
      • Jeanne Cambefort
        Hello, I m sorry I reply late. I think I can exploit my results by calculating the FRET Efficiency this way:
        Message 3 of 6 , May 17, 2012
        View Source
        • 0 Attachment
          Hello,

          I'm sorry I reply late.

          I think I can exploit my results by calculating the FRET Efficiency this way:
          http://www.msg.ucsf.edu/local/programs/cns1.3/tutorial/fret/fret_distribution_calculations/text.html
          I will make some calculations soon, because I just want to present results as
          correct as possible.

          Otherwise tihs is my log file :
                    ============================================================
                    |                                                          |
                    |            Crystallography & NMR System (CNS)            |
                    |                         CNSsolve                         |
                    |                                                          |
                    ============================================================
                     Version: 1.3
                     Status: General release
                    ============================================================
                     Written by: A.T.Brunger, P.D.Adams, G.M.Clore, W.L.DeLano,
                                 P.Gros, R.W.Grosse-Kunstleve,J.-S.Jiang,J.M.Krahn,
                                 J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read,
                                 L.M.Rice, G.F.Schroeder, T.Simonson, G.L.Warren.
                     Copyright (c) 1997-2010 Yale University
                    ============================================================
                     Running on machine: hostname unknown (Mac/Intel,64-bit)
                     Program started by: jeanne
                     Program started at: 12:04:51 on 16-May-2012
                    ============================================================

           FFT3C: Using FFTPACK4.1

           CNSsolve>{+ file: model_anneal.inp +}
           CNSsolve>{+ directory: general +}
           CNSsolve>{+ description: simulated annealing/molecular dynamics +}
           CNSsolve>{+ authors: Axel T. Brunger, Luke M. Rice and Paul D. Adams +}
           CNSsolve>{+ copyright: Yale University +}
           CNSsolve>
           CNSsolve>{+ reference: L.M. Rice and A.T. Brunger, Torsion Angle Dynamics:
           CNSsolve>              Reduced Variable Conformational Sampling Enhances
           CNSsolve>              Crystallographic Structure Refinement, Proteins: Structure,
           CNSsolve>              Function, and Genetics, 19, 277-290 (1994) +}
           CNSsolve>
           CNSsolve>{- Guidelines for using this file:
           CNSsolve>   - all strings must be quoted by double-quotes
           CNSsolve>   - logical variables (true/false) are not quoted
           CNSsolve>   - do not remove any evaluate statements from the file
           CNSsolve>   - the selections store1 through store3 are available for general use -}
           CNSsolve>
           CNSsolve>{- begin block parameter definition -} define(
           DEFINE>
           DEFINE>{============================ coordinates ============================}
           DEFINE>
           DEFINE>{* coordinate file *}
           DEFINE>{===>} coordinate_infile="generate_3HOS.pdb";
           DEFINE>
           DEFINE>{==================== molecular information ==========================}
           DEFINE>
           DEFINE>{* topology files *}
           DEFINE>{===>} topology_infile_1="CNS_TOPPAR:protein-allhdg5-4.top";
           DEFINE>{===>} topology_infile_2="CNS_TOPPAR:dna-rna-allatom-hj-opls.top";
           DEFINE>{===>} topology_infile_3="CNS_TOPPAR:5iu.top";
           DEFINE>{===>} topology_infile_4="CNS_TOPPAR:water-allhdg5-4.top";
           DEFINE>{===>} topology_infile_5="CNS_TOPPAR:ion.top";
           DEFINE>
           DEFINE>{* linkage files for linear, continuous polymers (protein, DNA, RNA) *}
           DEFINE>{===>} link_infile_1="CNS_TOPPAR:protein-allhdg5-4.link";
           DEFINE>{===>} link_infile_2="CNS_TOPPAR:dna-rna-pho.link";
           DEFINE>
           DEFINE>{* parameter files *}
           DEFINE>{===>} parameter_infile_1="CNS_TOPPAR:protein-allhdg5-4.param";
           DEFINE>{===>} parameter_infile_2="CNS_TOPPAR:dna-rna-allatom-hj-opls.param";
           DEFINE>{===>} parameter_infile_3="CNS_TOPPAR:5iu.param";
           DEFINE>{===>} parameter_infile_4="CNS_TOPPAR:water-allhdg5-4.param";
           DEFINE>{===>} parameter_infile_5="CNS_TOPPAR:ion.param";
           DEFINE>
           DEFINE>{* molecular topology file: optional (leave blank for auto generation) *}
           DEFINE>{*
           DEFINE>   Auto generation of the molecular topology from the coordinates should only
           DEFINE>   be used if:
           DEFINE>   (1) Each distinct protein, DNA, or RNA chain must have a separate segid
           DEFINE>       (or chainid if the chainid is non-blank).
           DEFINE>   (2) Each contiguous protein, RNA, or RNA chain must not be disrupted by
           DEFINE>       other types of residues or ligands.  Rather, these other residues
           DEFINE>       should be listed after protein, RNA/DNA chains.
           DEFINE>   (3) Disulphides are automatically detected based on distances between the sulfur atoms
           DEFINE>      (must be less than 3 A apart).
           DEFINE>   (4) Broken protein/RNA/DNA chains without terminii must be more than 2.5 A apart to be recognized as such.
           DEFINE>   (5) N-linked glycan links are automatically recognized if the bonded atoms are less than 2.5 A apart.
           DEFINE>   (6) Automatic generation cannot be used with alternate conformations.
           DEFINE>   For ligands, the user must make suitable topology and parameter files.
           DEFINE>   For non-standard covalent linkages, the custom patch file should be used.
           DEFINE>   Alternatively, the generate.inp or generate_easy.inp task files
           DEFINE>   can be used to generated the mtf prior to running this task file.
           DEFINE>    *}
           DEFINE>{===>} structure_infile="";
           DEFINE>
           DEFINE>{* for auto generation: extra linkages and modifications by custom patches *}
           DEFINE>{===>} patch_infile="";
           DEFINE>
           DEFINE>{===================== crystallographic symmetry =====================}
           DEFINE>
           DEFINE>{* use crystallographic symmetry *}
           DEFINE>{+ choice: true false +}
           DEFINE>{===>} use_cryst=false;
           DEFINE>
           DEFINE>{* space group *}
           DEFINE>{* use International Table conventions with subscripts substituted
           DEFINE>   by parenthesis *}
           DEFINE>{===>} sg="P2(1)2(1)2(1)";
           DEFINE>
           DEFINE>{* unit cell parameters in Angstroms and degrees *}
           DEFINE>{+ table: rows=1 "cell" cols=6 "a" "b" "c" "alpha" "beta" "gamma" +}
           DEFINE>{===>} a=61.76;
           DEFINE>{===>} b=40.73;
           DEFINE>{===>} c=26.74;
           DEFINE>{===>} alpha=90;
           DEFINE>{===>} beta=90;
           DEFINE>{===>} gamma=90;
           DEFINE>
           DEFINE>{=================== non-crystallographic symmetry ===================}
           DEFINE>
           DEFINE>{* NCS-restraints/constraints file *}
           DEFINE>{* see auxiliary/ncs.def *}
           DEFINE>{===>} ncs_infile="";
           DEFINE>
           DEFINE>{========================== atom selection ===========================}
           DEFINE>
           DEFINE>{* select atoms to be included *}
           DEFINE>{* it is essential to include hydrogen atoms if a free MD simulation is
           DEFINE>   being performed *}
           DEFINE>{* this should include all conformations if multiple conformations are used *}
           DEFINE>{===>} atom_select=(known);
           DEFINE>
           DEFINE>{* select fixed atoms *}
           DEFINE>{* note: isolated atoms and diatomic molecules are automatically
           DEFINE>   fixed during torsion angle dynamics. So, you don't have to
           DEFINE>   explicitly fix them here. *}
           DEFINE>{===>} atom_fixed=(none);
           DEFINE>
           DEFINE>{* select atoms to be harmonically restrained *}
           DEFINE>{===>} atom_harm=(none);
           DEFINE>
           DEFINE>{* harmonic restraint constant - for harmonically restrained atoms *}
           DEFINE>{===>} k_harmonic=10;
           DEFINE>
           DEFINE>{* atom selections for non-default rigid groups during torsion angle dynamics *}
           DEFINE>{* note: the selections must be non-overlapping *}
           DEFINE>{===>} atom_rigid_1=(none);
           DEFINE>{===>} atom_rigid_2=(none);
           DEFINE>{===>} atom_rigid_3=(none);
           DEFINE>{===>} atom_rigid_4=(none);
           DEFINE>{===>} atom_rigid_5=(none);
           DEFINE>{===>} atom_rigid_6=(none);
           DEFINE>{===>} atom_rigid_7=(none);
           DEFINE>{===>} atom_rigid_8=(none);
           DEFINE>{===>} atom_rigid_9=(none);
           DEFINE>{===>} atom_rigid_10=(none);
           DEFINE>! to add more groups add more numbered entries:
           DEFINE>!   {===>} atom_rigid_11=(none);
           DEFINE>!   {===>} atom_rigid_12=(none);
           DEFINE>!   {===>} atom_rigid_13=(none);
           DEFINE>! etc
           DEFINE>
           DEFINE>{* select atoms in alternate conformation 1 *}
           DEFINE>{===>} conf_1=(none);
           DEFINE>
           DEFINE>{* select atoms in alternate conformation 2 *}
           DEFINE>{===>} conf_2=(none);
           DEFINE>
           DEFINE>{* select atoms in alternate conformation 3 *}
           DEFINE>{===>} conf_3=(none);
           DEFINE>
           DEFINE>{* select atoms in alternate conformation 4 *}
           DEFINE>{===>} conf_4=(none);
           DEFINE>
           DEFINE>{* additional restraints file *}
           DEFINE>{* eg. auxiliary/dna-rna_restraints.def *}
           DEFINE>{===>} restraints_infile="";
           DEFINE>
           DEFINE>{====================== annealing parameters ========================}
           DEFINE>
           DEFINE>{* type of molecular dynamics *}
           DEFINE>{+ choice: "torsion" "cartesian" +}
           DEFINE>{===>} md_type="cartesian";
           DEFINE>
           DEFINE>{* annealing schedule *}
           DEFINE>{+ choice: "slowcool" "constant" +}
           DEFINE>{===>} md_scheme="constant";
           DEFINE>
           DEFINE>{* starting temperature *}
           DEFINE>{* used for both constant-temperature and slowcooling schemes *}
           DEFINE>{===>} temperature=300;
           DEFINE>
           DEFINE>{* temperature control method *}
           DEFINE>{* either coupling to a temperature bath or velocity scaling *}
           DEFINE>{+ choice: coupling scaling +}
           DEFINE>{===>} tcontrol="coupling";
           DEFINE>
           DEFINE>{* number of molecular dynamics steps *}
           DEFINE>{* only used for constant-temperature annealing schedule *}
           DEFINE>{===>} constant_steps=1000;
           DEFINE>
           DEFINE>{* drop in temperature (K) per cycle of dynamics *}
           DEFINE>{* only used for slowcooling annealing schedule *}
           DEFINE>{===>} cool_rate=25;
           DEFINE>
           DEFINE>{* molecular dynamics time step (ps) *}
           DEFINE>{===>} time_step=0.0005;
           DEFINE>
           DEFINE>{* number of minimization steps to regularize geometry before torsion md *}
           DEFINE>{===>} geometry_min=100;
           DEFINE>
           DEFINE>{* nonbonded cutoff (Angstroms) *}
           DEFINE>{===>} nonb_cutoff=13;
           DEFINE>
           DEFINE>{* dielectric constant *}
           DEFINE>{===>} dielectric=1;
           DEFINE>
           DEFINE>{* number of trials to carry out with different initial velocities *}
           DEFINE>{===>} num_trials=1;
           DEFINE>
           DEFINE>{* frequency of writing trajectory (in steps) *}
           DEFINE>{* this only applies to the constant temperature option *}
           DEFINE>{* a trajectory will not be written if this value is 0 or less *}
           DEFINE>{===>} traj_freq=100;
           DEFINE>
           DEFINE>{* seed for random number generator *}
           DEFINE>{* change to get different initial velocities *}
           DEFINE>{===>} seed=82364;
           DEFINE>
           DEFINE>{* torsion angle topology modification file *}
           DEFINE>{===>} torsion_infile="CNS_TOPPAR:torsionmdmods";
           DEFINE>
           DEFINE>{=========================== output files ============================}
           DEFINE>
           DEFINE>{* root name for output files *}
           DEFINE>{+ list:
           DEFINE>        coordinate files will be written: <output_root>_<n>.pdb
           DEFINE>        if the trajectory option is enabled (annealing schedule = constant and frequency > 0)
           DEFINE>             a CNS trajectory file will be written to: <output_root>_<n>_traj.crd,
           DEFINE>             the corresponding individual coordinates will be in <output_root>_<n>_traj_<m>.pdb
           DEFINE>             and a combined coordinate file (for display with VMD) with all
           DEFINE>             these coordinates appended will be in <output_root>_<n>_traj.pdb
           DEFINE>             where <n> is the trial number and <m> is the trajectory frame number. +}
           DEFINE>{===>} output_root="model_anneal_3HOS";
           DEFINE>
           DEFINE>{===========================================================================}
           DEFINE>{         things below this line do not normally need to be changed         }
           DEFINE>{         except for the torsion angle topology setup if you have           }
           DEFINE>{         molecules other than protein or nucleic acid                      }
           DEFINE>{===========================================================================}
           DEFINE>
           DEFINE> ) {- end block parameter definition -}
           CNSsolve>
           CNSsolve> checkversion 1.3
           Program version= 1.3 File version= 1.3
           CNSsolve>
           CNSsolve> evaluate ($log_level=quiet)
           Assuming literal string "QUIET"
           EVALUATE: symbol $LOG_LEVEL set to "QUIET" (string)
           CNSsolve>
           CNSsolve> if ( $log_level = verbose ) then
           NEXTCD: condition evaluated as false
           CNSsolve>   set message=normal echo=on end
           CNSsolve> else
           CNSsolve>   set message=off echo=off end

           automatically generating molecular topology

           ASSFIL: file generate_3HOS.pdb opened.
           SEGMNT-info: auto chain termination due to different segid.  336 residues were inserted into segid "A   "
           SEGMNT-info: auto chain termination due to different segid.  337 residues were inserted into segid "B   "
           SEGMNT-info: auto chain termination due to different segid.   25 residues were inserted into segid "C   "
           SEGMNT-info: auto chain termination due to different segid.   28 residues were inserted into segid "D   "
           SEGMNT-info: auto chain termination due to different segid.   25 residues were inserted into segid "E   "
           SEGMNT-info: auto chain termination due to different segid.   28 residues were inserted into segid "F   "
           SEGMNT-info: auto chain termination due to unavailable link.     1 residues were inserted into segid "A   "
           SEGMNT-info: chain termination due to END keyword.     1 residues were inserted into segid "    "
           %READC-ERR: atom A    243  ARG  HT1  not found in molecular structure
           %READC-ERR: atom A    243  ARG  HT2  not found in molecular structure
           %READC-ERR: atom A    243  ARG  HT3  not found in molecular structure
           %READC-ERR: atom B    243  ARG  HT1  not found in molecular structure
           %READC-ERR: atom B    243  ARG  HT2  not found in molecular structure
           %READC-ERR: atom B    243  ARG  HT3  not found in molecular structure
           link removed (applied DPEP): from A    237  to A    243
           link removed (applied DPEP): from B    238  to B    243
           disulphide added: from A    136  to A    336
           disulphide added: from B    136  to B    336
           unknown coordinates for atom: A    GLU  345  OXT
           unknown coordinates for atom: C    DG   4    O5T
           unknown coordinates for atom: D    DA   29   P  
           unknown coordinates for atom: D    DA   29   OP1
           unknown coordinates for atom: D    DA   29   OP2
           unknown coordinates for atom: D    DA   29   O5T
           unknown coordinates for atom: E    DG   4    O5T
           unknown coordinates for atom: F    DA   29   P  
           unknown coordinates for atom: F    DA   29   OP1
           unknown coordinates for atom: F    DA   29   OP2
           unknown coordinates for atom: F    DA   29   O5T

           %PARRDR-info: duplication of bond HC   NC2
           %PARRDR-info: duplication of bond OUF  SUF
           %PARRDR-info: duplication of angle CH2P CH2E HA 
           %PARRDR-info: duplication of angle OUF  SUF  OUF
           %PARRDR-info: duplication of nonbonded entry H  
           %PARRDR-info: duplication of nonbonded entry HA 
           %PARRDR-info: duplication of nonbonded entry HC 
           %PARRDR-info: duplication of nonbonded entry SUF
           %PARRDR-info: duplication of nonbonded entry OUF
           EFLAGS: the following energy flags are set
           EFLAGS: BOND ANGL DIHE IMPR VDW  ELEC
           %PARRDR-info: duplication of bond HC   NC2
           %PARRDR-info: duplication of bond OUF  SUF
           %PARRDR-info: duplication of angle CH2P CH2E HA 
           %PARRDR-info: duplication of angle OUF  SUF  OUF
           %PARRDR-info: duplication of nonbonded entry H  
           %PARRDR-info: duplication of nonbonded entry HA 
           %PARRDR-info: duplication of nonbonded entry HC 
           %PARRDR-info: duplication of nonbonded entry SUF
           %PARRDR-info: duplication of nonbonded entry OUF
           -----nonbonded-list-options-------------------------------
           | CUTNb=  13.000 TOLErance=   0.500 WMIN=   1.500 ATOM   |
           | INHIbit=   0.250                                       |
           -----electrostatic options--------------------------------
           | EPS=   1.000 E14Fac=   1.000 CDIElectric POTEN SHIFt   |
           -----van der Waals options--------------------------------
           | VSWItch                                                |
           -----switching /shifting parameters-----------------------
           | CTONNB=  11.000 CTOFNB=  12.000                        |
           -----exclusion list options-------------------------------
           | NBXMOD=   5                                            |
           ----------------------------------------------------------
           %PARRDR-info: duplication of bond HC   NC2
           %PARRDR-info: duplication of bond OUF  SUF
           %PARRDR-info: duplication of angle CH2P CH2E HA 
           %PARRDR-info: duplication of angle OUF  SUF  OUF
           %PARRDR-info: duplication of nonbonded entry H  
           %PARRDR-info: duplication of nonbonded entry HA 
           %PARRDR-info: duplication of nonbonded entry HC 
           %PARRDR-info: duplication of nonbonded entry SUF
           %PARRDR-info: duplication of nonbonded entry OUF
           CONNECt: selected atoms form     10 covalently disconnected set(s)

           list of isolated (non-covalently bonded) atoms:

           list of isolated (non-covalently bonded) di-atomic molecules:
           --none--
           %PARRDR-info: duplication of bond HC   NC2
           %PARRDR-info: duplication of bond OUF  SUF
           %PARRDR-info: duplication of angle CH2P CH2E HA 
           %PARRDR-info: duplication of angle OUF  SUF  OUF
           %PARRDR-info: duplication of nonbonded entry H  
           %PARRDR-info: duplication of nonbonded entry HA 
           %PARRDR-info: duplication of nonbonded entry HC 
           %PARRDR-info: duplication of nonbonded entry SUF
           %PARRDR-info: duplication of nonbonded entry OUF
           DCART: temperature coupling (TCOUpling) enabled
          REMARK line 612, time_step = 0.0005
           CENMAS: Information about center of free masses
                   position [A]          :     29.45350    -10.87427     -3.67022
                   velocity [A/ps]       :      0.00390      0.00974     -0.03693
                   ang. mom. [amu A/ps]  : -35462.68696-354492.11735  14929.71768
                   kin. ener. [Kcal/mol] :      0.19889
           ROTSTP: CM translation and rotation removed.
           CENMAS: Information about center of free masses
                   position [A]          :     29.45350    -10.87427     -3.67022
                   velocity [A/ps]       :      0.00000      0.00000      0.00000
                   ang. mom. [amu A/ps]  :      0.00000      0.00000      0.00000
                   kin. ener. [Kcal/mol] :      0.00000
           NBONDS: generating intra-molecular exclusion list with mode= 5
           MAKINB: mode   5 found  44023 exclusions and  36859 interactions(1-4)
           %atoms "A   -24  -THR -HG23" and "A   -27  -GLU -HB2 " only  1.21 A apart
           %atoms "A   -24  -THR -O   " and "A   -28  -SER -HN  " only  1.38 A apart
           %atoms "A   -46  -CYS -HN  " and "A   -46  -CYS -HG  " only  1.48 A apart
           %atoms "A   -50  -PHE -HA  " and "A   -53  -PHE -HD2 " only  1.40 A apart
           %atoms "A   -88  -THR -HN  " and "A   -91  -GLN -HE21" only  1.11 A apart
           %atoms "A   -100 -GLN -HE22" and "C   -9   -DA  -H61 " only  1.40 A apart
           %atoms "A   -106 -ARG -HG1 " and "A   -106 -ARG -HH21" only  1.28 A apart
           %atoms "A   -146 -LYS -HA  " and "A   -146 -LYS -HE1 " only  1.45 A apart
           %atoms "A   -150 -HIS -HA  " and "A   -199 -GLN -HE22" only  1.37 A apart
           %atoms "A   -154 -THR -HG1 " and "A   -155 -GLY -HN  " only  1.44 A apart
           %atoms "A   -166 -LYS -HN  " and "A   -166 -LYS -HD1 " only  1.14 A apart
           %atoms "A   -166 -LYS -HD2 " and "A   -297 -GLU -HB1 " only  1.46 A apart
           %atoms "A   -170 -SER -HB1 " and "B   -86  -ALA -HB1 " only  1.45 A apart
           %atoms "A   -174 -PRO -HA  " and "B   -113 -ILE -HD12" only  1.32 A apart
           %atoms "A   -191 -THR -HB  " and "A   -207 -LEU -HD11" only  1.36 A apart
           %atoms "A   -282 -PRO -HG1 " and "A   -329 -LEU -HD22" only  1.40 A apart
           %atoms "A   -284 -ASP -HA  " and "A   -288 -PHE -HD2 " only  1.33 A apart
           %atoms "A   -286 -HIS -HD1 " and "A   -328 -LYS -HZ1 " only  1.39 A apart
           %atoms "A   -337 -VAL -O   " and "A   -340 -ASP -HN  " only  1.40 A apart
           %atoms "B   -8   -LYS -HN  " and "B   -9   -GLU -HN  " only  1.49 A apart
           %atoms "B   -12  -ARG -HH21" and "B   -13  -THR -HG1 " only  1.43 A apart
           %atoms "B   -40  -VAL -HG21" and "B   -41  -PRO -HD2 " only  1.40 A apart
           %atoms "B   -42  -THR -HG1 " and "B   -45  -THR -HN  " only  1.49 A apart
           %atoms "B   -63  -LYS -HD1 " and "B   -64  -GLU -HN  " only  1.48 A apart
           %atoms "B   -100 -GLN -HB1 " and "B   -100 -GLN -HE21" only  1.49 A apart
           %atoms "B   -124 -LEU -HD11" and "B   -132 -ARG -HH11" only  1.48 A apart
           %atoms "B   -136 -CYS -HB1 " and "B   -333 -TRP -HB1 " only  1.44 A apart
           %atoms "B   -141 -SER -HG  " and "B   -145 -ARG -HH11" only  1.43 A apart
           %atoms "B   -153 -VAL -HN  " and "B   -245 -ILE -O   " only  1.46 A apart
           %atoms "B   -157 -GLU -HB1 " and "B   -194 -CYS -HB1 " only  1.40 A apart
           %atoms "B   -166 -LYS -HN  " and "B   -166 -LYS -HD1 " only  1.23 A apart
           %atoms "B   -198 -ASP -O   " and "B   -201 -GLY -HN  " only  1.46 A apart
           %atoms "B   -202 -VAL -HG21" and "B   -203 -ILE -HN  " only  1.08 A apart
           %atoms "B   -210 -PRO -HD1 " and "B   -303 -TYR -HD1 " only  1.40 A apart
           %atoms "B   -215 -ASN -OD1 " and "B   -218 -ARG -HN  " only  1.45 A apart
           %atoms "B   -223 -LEU -HN  " and "B   -223 -LEU -HD12" only  1.41 A apart
           %atoms "B   -225 -ASN -HN  " and "B   -225 -ASN -HD21" only  1.37 A apart
           %atoms "B   -246 -PHE -HE2 " and "B   -248 -HIS -HD1 " only  1.38 A apart
           %atoms "B   -271 -LEU -HD23" and "B   -272 -PRO -HD2 " only  1.08 A apart
           %atoms "B   -284 -ASP -HA  " and "B   -288 -PHE -HD2 " only  1.44 A apart
           %atoms "B   -288 -PHE -O   " and "B   -292 -GLY -HN  " only  1.49 A apart
           %atoms "B   -337 -VAL -O   " and "B   -340 -ASP -HN  " only  1.28 A apart
           %atoms "C   -13  -DG  -H2''" and "C   -14  -DT  -H5' " only  1.29 A apart
           %atoms "C   -18  -DA  -H2''" and "C   -19  -DA  -H8  " only  1.45 A apart
           %atoms "C   -25  -DG  -H1  " and "D   -32  -DC  -H42 " only  1.13 A apart
           %atoms "D   -31  -DA  -H2''" and "D   -32  -DC  -H5''" only  1.37 A apart
           %atoms "D   -34  -DA  -H2''" and "D   -35  -DC  -H5''" only  1.41 A apart
           %atoms "D   -42  -DT  -H5''" and "D   -42  -DT  -H6  " only  1.22 A apart
           %atoms "D   -43  -DA  -H2''" and "D   -44  -DC  -H5''" only  1.20 A apart
           %atoms "D   -45  -DT  -H5' " and "D   -45  -DT  -H6  " only  1.35 A apart
           %atoms "D   -46  -DT  -H2''" and "D   -47  -DG  -H5' " only  1.02 A apart
           %atoms "D   -51  -DA  -H2''" and "D   -52  -DC  -H5' " only  1.27 A apart
           %atoms "D   -54  -DT  -H71 " and "D   -55  -DG  -H1  " only  1.28 A apart
           %atoms "E   -12  -DA  -H2''" and "E   -13  -DG  -H5''" only  1.28 A apart
           %atoms "E   -22  -DG  -H5' " and "E   -22  -DG  -H8  " only  1.50 A apart
           %atoms "E   -26  -DT  -H2''" and "E   -27  -DT  -H5' " only  1.27 A apart
           %atoms "F   -33  -DG  -H2''" and "F   -34  -DA  -H5' " only  1.49 A apart
           %atoms "F   -36  -DA  -H2''" and "F   -37  -DT  -H5' " only  1.36 A apart
           %atoms "F   -38  -DT  -H2''" and "F   -39  -DT  -H5''" only  1.31 A apart
           %atoms "F   -41  -DA  -H1' " and "F   -42  -DT  -H5''" only  1.45 A apart
           %atoms "F   -53  -DC  -H2''" and "F   -54  -DT  -H5' " only  1.25 A apart
           %atoms "F   -54  -DT  -H6  " and "F   -54  -DT  -H2' " only  1.33 A apart
           NBONDS: found  3741222 intra-atom interactions
           NBONDS: found       62 nonbonded violations
           -------------------------- Cartesian dynamics start ---------------------------
           | E(kin)+E(total)=37472.511       E(kin)=12984.605     temperature=300.090    |
           | Etotal =24487.906  grad(E)=94.905     E(BOND)=2964.078   E(ANGL)=12393.175  |
           | E(DIHE)=4236.691   E(IMPR)=21998.395  E(VDW )=4034.192   E(ELEC)=-21138.624 |
           -------------------------------------------------------------------------------
           %atoms "A   -24  -THR -O   " and "A   -28  -SER -HN  " only  1.39 A apart
           %atoms "A   -46  -CYS -HN  " and "A   -46  -CYS -HG  " only  1.46 A apart
           %atoms "A   -50  -PHE -HA  " and "A   -53  -PHE -HD2 " only  1.42 A apart
           %atoms "A   -88  -THR -HN  " and "A   -91  -GLN -HE21" only  1.12 A apart
           %atoms "A   -100 -GLN -HE22" and "C   -9   -DA  -H61 " only  1.40 A apart
           %atoms "A   -106 -ARG -HG1 " and "A   -106 -ARG -HH21" only  1.30 A apart
           %atoms "A   -146 -LYS -HA  " and "A   -146 -LYS -HE1 " only  1.49 A apart
           %atoms "A   -150 -HIS -HA  " and "A   -199 -GLN -HE22" only  1.39 A apart
           %atoms "A   -154 -THR -HG1 " and "A   -155 -GLY -HN  " only  1.45 A apart
           %atoms "A   -166 -LYS -HN  " and "A   -166 -LYS -HD1 " only  1.26 A apart
           %atoms "A   -166 -LYS -HD2 " and "A   -297 -GLU -HB1 " only  1.46 A apart
           %atoms "A   -174 -PRO -HA  " and "B   -113 -ILE -HD12" only  1.43 A apart
           %atoms "A   -191 -THR -HB  " and "A   -207 -LEU -HD11" only  1.42 A apart
           %atoms "A   -282 -PRO -HG1 " and "A   -329 -LEU -HD22" only  1.43 A apart
           %atoms "A   -284 -ASP -HA  " and "A   -288 -PHE -HD2 " only  1.43 A apart
           %atoms "A   -286 -HIS -HD1 " and "A   -328 -LYS -HZ1 " only  1.39 A apart
           %atoms "A   -337 -VAL -O   " and "A   -340 -ASP -HN  " only  1.41 A apart
           %atoms "B   -12  -ARG -HH21" and "B   -13  -THR -HG1 " only  1.45 A apart
           %atoms "B   -15  -LEU -HN  " and "B   -15  -LEU -HD11" only  1.49 A apart
           %atoms "B   -40  -VAL -HG21" and "B   -41  -PRO -HD2 " only  1.44 A apart
           %atoms "B   -63  -LYS -HD1 " and "B   -64  -GLU -HN  " only  1.49 A apart
           %atoms "B   -100 -GLN -HB1 " and "B   -100 -GLN -HE21" only  1.49 A apart
           %atoms "B   -124 -LEU -HD11" and "B   -132 -ARG -HH11" only  1.47 A apart
           %atoms "B   -136 -CYS -HB1 " and "B   -333 -TRP -HB1 " only  1.45 A apart
           %atoms "B   -141 -SER -HG  " and "B   -145 -ARG -HH11" only  1.43 A apart
           %atoms "B   -153 -VAL -HN  " and "B   -245 -ILE -O   " only  1.45 A apart
           %atoms "B   -157 -GLU -HB1 " and "B   -194 -CYS -HB1 " only  1.46 A apart
           %atoms "B   -166 -LYS -HN  " and "B   -166 -LYS -HD1 " only  1.26 A apart
           %atoms "B   -198 -ASP -O   " and "B   -201 -GLY -HN  " only  1.47 A apart
           %atoms "B   -202 -VAL -HG21" and "B   -203 -ILE -HN  " only  1.32 A apart
           %atoms "B   -210 -PRO -HD1 " and "B   -303 -TYR -HD1 " only  1.44 A apart
           %atoms "B   -215 -ASN -OD1 " and "B   -218 -ARG -HN  " only  1.44 A apart
           %atoms "B   -223 -LEU -HN  " and "B   -223 -LEU -HD12" only  1.41 A apart
           %atoms "B   -225 -ASN -HN  " and "B   -225 -ASN -HD21" only  1.37 A apart
           %atoms "B   -246 -PHE -HE2 " and "B   -248 -HIS -HD1 " only  1.36 A apart
           %atoms "B   -284 -ASP -HA  " and "B   -288 -PHE -HD2 " only  1.49 A apart
           %atoms "B   -288 -PHE -O   " and "B   -292 -GLY -HN  " only  1.50 A apart
           %atoms "B   -337 -VAL -O   " and "B   -340 -ASP -HN  " only  1.31 A apart
           %atoms "C   -13  -DG  -H2''" and "C   -14  -DT  -H5' " only  1.29 A apart
           %atoms "C   -18  -DA  -H2''" and "C   -19  -DA  -H8  " only  1.45 A apart
           %atoms "C   -25  -DG  -H1  " and "D   -32  -DC  -H42 " only  1.15 A apart
           %atoms "D   -31  -DA  -H2''" and "D   -32  -DC  -H5''" only  1.38 A apart
           %atoms "D   -34  -DA  -H2''" and "D   -35  -DC  -H5''" only  1.40 A apart
           %atoms "D   -42  -DT  -H5''" and "D   -42  -DT  -H6  " only  1.22 A apart
           %atoms "D   -43  -DA  -H2''" and "D   -44  -DC  -H5''" only  1.21 A apart
           %atoms "D   -45  -DT  -H5' " and "D   -45  -DT  -H6  " only  1.35 A apart
           %atoms "D   -46  -DT  -H2''" and "D   -47  -DG  -H5' " only  1.02 A apart
           %atoms "D   -51  -DA  -H2''" and "D   -52  -DC  -H5' " only  1.27 A apart
           %atoms "D   -54  -DT  -H71 " and "D   -55  -DG  -H1  " only  1.29 A apart
           %atoms "E   -12  -DA  -H2''" and "E   -13  -DG  -H5''" only  1.28 A apart
           %atoms "E   -22  -DG  -H5' " and "E   -22  -DG  -H8  " only  1.49 A apart
           %atoms "E   -26  -DT  -H2''" and "E   -27  -DT  -H5' " only  1.27 A apart
           %atoms "F   -33  -DG  -H2''" and "F   -34  -DA  -H5' " only  1.49 A apart
           %atoms "F   -36  -DA  -H2''" and "F   -37  -DT  -H5' " only  1.35 A apart
           %atoms "F   -38  -DT  -H2''" and "F   -39  -DT  -H5''" only  1.29 A apart
           %atoms "F   -41  -DA  -H1' " and "F   -42  -DT  -H5''" only  1.45 A apart
           %atoms "F   -53  -DC  -H2''" and "F   -54  -DT  -H5' " only  1.24 A apart
           %atoms "F   -54  -DT  -H6  " and "F   -54  -DT  -H2' " only  1.32 A apart
           NBONDS: found  3741229 intra-atom interactions
           NBONDS: found       58 nonbonded violations
           %atoms "A   -24  -THR -O   " and "A   -28  -SER -HN  " only  1.40 A apart
           %atoms "A   -46  -CYS -HN  " and "A   -46  -CYS -HG  " only  1.45 A apart
           %atoms "A   -50  -PHE -HA  " and "A   -53  -PHE -HD2 " only  1.47 A apart
           %atoms "A   -88  -THR -HN  " and "A   -91  -GLN -HE21" only  1.15 A apart
           %atoms "A   -100 -GLN -HE22" and "C   -9   -DA  -H61 " only  1.41 A apart
           %atoms "A   -106 -ARG -HG1 " and "A   -106 -ARG -HH21" only  1.33 A apart
           %atoms "A   -150 -HIS -HA  " and "A   -199 -GLN -HE22" only  1.40 A apart
           %atoms "A   -154 -THR -HG1 " and "A   -155 -GLY -HN  " only  1.46 A apart
           %atoms "A   -166 -LYS -HN  " and "A   -166 -LYS -HD1 " only  1.39 A apart
           %atoms "A   -166 -LYS -HD2 " and "A   -297 -GLU -HB1 " only  1.49 A apart
           %atoms "A   -282 -PRO -HG1 " and "A   -329 -LEU -HD22" only  1.49 A apart
           %atoms "A   -286 -HIS -HD1 " and "A   -328 -LYS -HZ1 " only  1.41 A apart
           %atoms "A   -337 -VAL -O   " and "A   -340 -ASP -HN  " only  1.42 A apart
           %atoms "B   -12  -ARG -HH21" and "B   -13  -THR -HG1 " only  1.46 A apart
           %atoms "B   -15  -LEU -HN  " and "B   -15  -LEU -HD11" only  1.48 A apart
           %atoms "B   -63  -LYS -HD1 " and "B   -64  -GLU -HN  " only  1.49 A apart
           %atoms "B   -100 -GLN -HB1 " and "B   -100 -GLN -HE21" only  1.48 A apart
           %atoms "B   -124 -LEU -HD11" and "B   -132 -ARG -HH11" only  1.47 A apart
           %atoms "B   -136 -CYS -HB1 " and "B   -333 -TRP -HB1 " only  1.49 A apart
           %atoms "B   -141 -SER -HG  " and "B   -145 -ARG -HH11" only  1.44 A apart
           %atoms "B   -153 -VAL -HN  " and "B   -245 -ILE -O   " only  1.44 A apart
           %atoms "B   -166 -LYS -HN  " and "B   -166 -LYS -HD1 " only  1.32 A apart
           %atoms "B   -198 -ASP -O   " and "B   -201 -GLY -HN  " only  1.48 A apart
           %atoms "B   -215 -ASN -OD1 " and "B   -218 -ARG -HN  " only  1.44 A apart
           %atoms "B   -223 -LEU -HN  " and "B   -223 -LEU -HD12" only  1.42 A apart
           %atoms "B   -225 -ASN -HN  " and "B   -225 -ASN -HD21" only  1.37 A apart
           %atoms "B   -246 -PHE -HE2 " and "B   -248 -HIS -HD1 " only  1.35 A apart
           %atoms "B   -337 -VAL -O   " and "B   -340 -ASP -HN  " only  1.34 A apart
           %atoms "C   -13  -DG  -H2''" and "C   -14  -DT  -H5' " only  1.29 A apart
           %atoms "C   -18  -DA  -H2''" and "C   -19  -DA  -H8  " only  1.45 A apart
           %atoms "C   -25  -DG  -H1  " and "D   -32  -DC  -H42 " only  1.17 A apart
           %atoms "D   -31  -DA  -H2''" and "D   -32  -DC  -H5' " only  1.50 A apart
           %atoms "D   -31  -DA  -H2''" and "D   -32  -DC  -H5''" only  1.39 A apart
           %atoms "D   -34  -DA  -H2''" and "D   -35  -DC  -H5''" only  1.40 A apart
           %atoms "D   -42  -DT  -H5''" and "D   -42  -DT  -H6  " only  1.22 A apart
           %atoms "D   -43  -DA  -H2''" and "D   -44  -DC  -H5''" only  1.21 A apart
           %atoms "D   -45  -DT  -H5' " and "D   -45  -DT  -H6  " only  1.34 A apart
           %atoms "D   -46  -DT  -H2''" and "D   -47  -DG  -H5' " only  1.02 A apart
           %atoms "D   -51  -DA  -H2''" and "D   -52  -DC  -H5' " only  1.28 A apart
           %atoms "D   -54  -DT  -H71 " and "D   -55  -DG  -H1  " only  1.30 A apart
           %atoms "E   -12  -DA  -H2''" and "E   -13  -DG  -H5''" only  1.28 A apart
           %atoms "E   -22  -DG  -H5' " and "E   -22  -DG  -H8  " only  1.48 A apart
           %atoms "E   -26  -DT  -H2''" and "E   -27  -DT  -H5' " only  1.28 A apart
           %atoms "F   -33  -DG  -H2''" and "F   -34  -DA  -H5' " only  1.48 A apart
           %atoms "F   -36  -DA  -H2''" and "F   -37  -DT  -H5' " only  1.34 A apart
           %atoms "F   -38  -DT  -H2''" and "F   -39  -DT  -H5''" only  1.28 A apart
           %atoms "F   -41  -DA  -H1' " and "F   -42  -DT  -H5''" only  1.46 A apart
           %atoms "F   -53  -DC  -H2''" and "F   -54  -DT  -H5' " only  1.24 A apart
           %atoms "F   -54  -DT  -H6  " and "F   -54  -DT  -H2' " only  1.32 A apart
           NBONDS: found  3741253 intra-atom interactions
           NBONDS: found       49 nonbonded violations
           %atoms "A   -24  -THR -O   " and "A   -28  -SER -HN  " only  1.41 A apart
           %atoms "A   -46  -CYS -HN  " and "A   -46  -CYS -HG  " only  1.44 A apart
           %atoms "A   -88  -THR -HN  " and "A   -91  -GLN -HE21" only  1.18 A apart
           %atoms "A   -100 -GLN -HE22" and "C   -9   -DA  -H61 " only  1.42 A apart
           %atoms "A   -106 -ARG -HG1 " and "A   -106 -ARG -HH21" only  1.36 A apart
           %atoms "A   -150 -HIS -HA  " and "A   -199 -GLN -HE22" only  1.42 A apart
           %atoms "A   -154 -THR -HG1 " and "A   -155 -GLY -HN  " only  1.47 A apart
           %atoms "A   -166 -LYS -HN  " and "A   -166 -LYS -HD1 " only  1.49 A apart
           %atoms "A   -286 -HIS -HD1 " and "A   -328 -LYS -HZ1 " only  1.43 A apart
           %atoms "A   -337 -VAL -O   " and "A   -340 -ASP -HN  " only  1.44 A apart
           %atoms "B   -12  -ARG -HH21" and "B   -13  -THR -HG1 " only  1.47 A apart
           %atoms "B   -15  -LEU -HN  " and "B   -15  -LEU -HD11" only  1.48 A apart
           %atoms "B   -29  -HIS -HD1 " and "B   -43  -VAL -HA  " only  1.50 A apart
           %atoms "B   -100 -GLN -HB1 " and "B   -100 -GLN -HE21" only  1.49 A apart
           %atoms "B   -124 -LEU -HD11" and "B   -132 -ARG -HH11" only  1.47 A apart
           %atoms "B   -141 -SER -HG  " and "B   -145 -ARG -HH11" only  1.45 A apart
           %atoms "B   -153 -VAL -HN  " and "B   -245 -ILE -O   " only  1.43 A apart
           %atoms "B   -166 -LYS -HN  " and "B   -166 -LYS -HD1 " only  1.37 A apart
           %atoms "B   -198 -ASP -O   " and "B   -201 -GLY -HN  " only  1.49 A apart
           %atoms "B   -215 -ASN -OD1 " and "B   -218 -ARG -HN  " only  1.44 A apart
           %atoms "B   -223 -LEU -HN  " and "B   -223 -LEU -HD12" only  1.43 A apart
           %atoms "B   -225 -ASN -HN  " and "B   -225 -ASN -HD21" only  1.37 A apart
           %atoms "B   -246 -PHE -HE2 " and "B   -248 -HIS -HD1 " only  1.36 A apart
           %atoms "B   -337 -VAL -O   " and "B   -340 -ASP -HN  " only  1.37 A apart
           %atoms "C   -13  -DG  -H2''" and "C   -14  -DT  -H5' " only  1.29 A apart
           %atoms "C   -18  -DA  -H2''" and "C   -19  -DA  -H8  " only  1.45 A apart
           %atoms "C   -25  -DG  -H1  " and "D   -32  -DC  -H42 " only  1.19 A apart
           %atoms "D   -31  -DA  -H2''" and "D   -32  -DC  -H5' " only  1.48 A apart
           %atoms "D   -31  -DA  -H2''" and "D   -32  -DC  -H5''" only  1.39 A apart
           %atoms "D   -34  -DA  -H2''" and "D   -35  -DC  -H5''" only  1.39 A apart
           %atoms "D   -42  -DT  -H5''" and "D   -42  -DT  -H6  " only  1.22 A apart
           %atoms "D   -43  -DA  -H2''" and "D   -44  -DC  -H5''" only  1.21 A apart
           %atoms "D   -45  -DT  -H5' " and "D   -45  -DT  -H6  " only  1.34 A apart
           %atoms "D   -46  -DT  -H2''" and "D   -47  -DG  -H5' " only  1.03 A apart
           %atoms "D   -51  -DA  -H2''" and "D   -52  -DC  -H5' " only  1.28 A apart
           %atoms "D   -54  -DT  -H71 " and "D   -55  -DG  -H1  " only  1.30 A apart
           %atoms "E   -12  -DA  -H2''" and "E   -13  -DG  -H5''" only  1.29 A apart
           %atoms "E   -22  -DG  -H5' " and "E   -22  -DG  -H8  " only  1.49 A apart
           %atoms "E   -26  -DT  -H2''" and "E   -27  -DT  -H5' " only  1.28 A apart
           %atoms "F   -33  -DG  -H2''" and "F   -34  -DA  -H5' " only  1.48 A apart
           %atoms "F   -36  -DA  -H2''" and "F   -37  -DT  -H5' " only  1.34 A apart
           %atoms "F   -38  -DT  -H2''" and "F   -39  -DT  -H5''" only  1.28 A apart
           %atoms "F   -41  -DA  -H1' " and "F   -42  -DT  -H5''" only  1.46 A apart
           %atoms "F   -53  -DC  -H2''" and "F   -54  -DT  -H5' " only  1.24 A apart
           %atoms "F   -54  -DT  -H6  " and "F   -54  -DT  -H2' " only  1.32 A apart
           NBONDS: found  3741318 intra-atom interactions
           NBONDS: found       45 nonbonded violations
           %atoms "A   -7   -ASN -HD22" and "A   -9   -GLU -HB1 " only  1.49 A apart
           %atoms "A   -24  -THR -O   " and "A   -28  -SER -HN  " only  1.42 A apart
           %atoms "A   -46  -CYS -HN  " and "A   -46  -CYS -HG  " only  1.44 A apart
           %atoms "A   -65  -HIS -HB2 " and "A   -66  -GLY -HN  " only  1.50 A apart
           %atoms "A   -88  -THR -HN  " and "A   -91  -GLN -HE21" only  1.22 A apart
           %atoms "A   -100 -GLN -HE22" and "C   -9   -DA  -H61 " only  1.42 A apart
           %atoms "A   -106 -ARG -HG1 " and "A   -106 -ARG -HH21" only  1.38 A apart
           %atoms "A   -150 -HIS -HA  " and "A   -199 -GLN -HE22" only  1.44 A apart
           %atoms "A   -154 -THR -HG1 " and "A   -155 -GLY -HN  " only  1.48 A apart
           %atoms "A   -286 -HIS -HD1 " and "A   -328 -LYS -HZ1 " only  1.47 A apart
           %atoms "A   -337 -VAL -O   " and "A   -340 -ASP -HN  " only  1.47 A apart
           %atoms "B   -12  -ARG -HH21" and "B   -13  -THR -HG1 " only  1.50 A apart
           %atoms "B   -15  -LEU -HN  " and "B   -15  -LEU -HD11" only  1.49 A apart
           %atoms "B   -101 -GLN -HG1 " and "F   -46  -DT  -H71 " only  1.49 A apart
           %atoms "B   -124 -LEU -HD11" and "B   -132 -ARG -HH11" only  1.48 A apart
           %atoms "B   -153 -VAL -HN  " and "B   -245 -ILE -O   " only  1.44 A apart
           %atoms "B   -166 -LYS -HN  " and "B   -166 -LYS -HD1 " only  1.42 A apart
           %atoms "B   -198 -ASP -O   " and "B   -201 -GLY -HN  " only  1.50 A apart
           %atoms "B   -202 -VAL -HG21" and "B   -203 -ILE -HN  " only  1.48 A apart
           %atoms "B   -215 -ASN -OD1 " and "B   -218 -ARG -HN  " only  1.46 A apart
           %atoms "B   -223 -LEU -HN  " and "B   -223 -LEU -HD12" only  1.43 A apart
           %atoms "B   -225 -ASN -HN  " and "B   -225 -ASN -HD21" only  1.37 A apart
           %atoms "B   -246 -PHE -HE2 " and "B   -248 -HIS -HD1 " only  1.41 A apart
           %atoms "B   -337 -VAL -O   " and "B   -340 -ASP -HN  " only  1.41 A apart
           %atoms "C   -13  -DG  -H2''" and "C   -14  -DT  -H5' " only  1.30 A apart
           %atoms "C   -18  -DA  -H2''" and "C   -19  -DA  -H8  " only  1.46 A apart
           %atoms "C   -19  -DA  -H2' " and "C   -20  -DA  -H8  " only  1.50 A apart
           %atoms "C   -25  -DG  -H1  " and "D   -32  -DC  -H42 " only  1.23 A apart
           %atoms "D   -31  -DA  -H2''" and "D   -32  -DC  -H5' " only  1.46 A apart
           %atoms "D   -31  -DA  -H2''" and "D   -32  -DC  -H5''" only  1.39 A apart
           %atoms "D   -34  -DA  -H2''" and "D   -35  -DC  -H5''" only  1.37 A apart
           %atoms "D   -42  -DT  -H5''" and "D   -42  -DT  -H6  " only  1.19 A apart
           %atoms "D   -43  -DA  -H2''" and "D   -44  -DC  -H5''" only  1.20 A apart
           %atoms "D   -45  -DT  -H5' " and "D   -45  -DT  -H6  " only  1.34 A apart
           %atoms "D   -46  -DT  -H2''" and "D   -47  -DG  -H5' " only  1.04 A apart
           %atoms "D   -51  -DA  -H2''" and "D   -52  -DC  -H5' " only  1.28 A apart
           %atoms "D   -54  -DT  -H71 " and "D   -55  -DG  -H1  " only  1.29 A apart
           %atoms "E   -12  -DA  -H2''" and "E   -13  -DG  -H5''" only  1.29 A apart
           %atoms "E   -26  -DT  -H2''" and "E   -27  -DT  -H5' " only  1.26 A apart
           %atoms "F   -33  -DG  -H2''" and "F   -34  -DA  -H5' " only  1.49 A apart
           %atoms "F   -36  -DA  -H2''" and "F   -37  -DT  -H5' " only  1.33 A apart
           %atoms "F   -38  -DT  -H2''" and "F   -39  -DT  -H5''" only  1.29 A apart
           %atoms "F   -41  -DA  -H1' " and "F   -42  -DT  -H5''" only  1.45 A apart
           %atoms "F   -53  -DC  -H2''" and "F   -54  -DT  -H5' " only  1.23 A apart
           %atoms "F   -54  -DT  -H6  " and "F   -54  -DT  -H2' " only  1.34 A apart
           NBONDS: found  3741454 intra-atom interactions
           NBONDS: found       45 nonbonded violations
           %atoms "A   -7   -ASN -HD22" and "A   -9   -GLU -HB1 " only  1.48 A apart
           %atoms "A   -24  -THR -O   " and "A   -28  -SER -HN  " only  1.43 A apart
           %atoms "A   -46  -CYS -HN  " and "A   -46  -CYS -HG  " only  1.46 A apart
           %atoms "A   -65  -HIS -HB2 " and "A   -66  -GLY -HN  " only  1.45 A apart
           %atoms "A   -88  -THR -HN  " and "A   -91  -GLN -HE21" only  1.22 A apart
           %atoms "A   -100 -GLN -HE22" and "C   -9   -DA  -H61 " only  1.41 A apart
           %atoms "A   -106 -ARG -HG1 " and "A   -106 -ARG -HH21" only  1.34 A apart
           %atoms "A   -150 -HIS -HA  " and "A   -199 -GLN -HE22" only  1.44 A apart
           %atoms "A   -154 -THR -HG1 " and "A   -155 -GLY -HN  " only  1.49 A apart
           %atoms "A   -166 -LYS -HN  " and "A   -166 -LYS -HD1 " only  1.44 A apart
           %atoms "A   -170 -SER -HB1 " and "B   -86  -ALA -HB1 " only  1.48 A apart
           %atoms "A   -191 -THR -HB  " and "A   -207 -LEU -HD11" only  1.47 A apart
           %atoms "A   -284 -ASP -HA  " and "A   -288 -PHE -HD2 " only  1.43 A apart
           %atoms "A   -337 -VAL -O   " and "A   -340 -ASP -HN  " only  1.49 A apart
           %atoms "B   -8   -LYS -HN  " and "B   -9   -GLU -HN  " only  1.49 A apart
           %atoms "B   -124 -LEU -HD11" and "B   -132 -ARG -HH11" only  1.48 A apart
           %atoms "B   -125 -ASN -O   " and "B   -128 -GLN -HN  " only  1.50 A apart
           %atoms "B   -153 -VAL -HN  " and "B   -245 -ILE -O   " only  1.48 A apart
           %atoms "B   -157 -GLU -HB1 " and "B   -194 -CYS -HB1 " only  1.44 A apart
           %atoms "B   -166 -LYS -HN  " and "B   -166 -LYS -HD1 " only  1.36 A apart
           %atoms "B   -197 -TRP -HE1 " and "B   -283 -SER -HB1 " only  1.48 A apart
           %atoms "B   -202 -VAL -HG21" and "B   -203 -ILE -HN  " only  1.17 A apart
           %atoms "B   -215 -ASN -OD1 " and "B   -218 -ARG -HN  " only  1.49 A apart
           %atoms "B   -223 -LEU -HN  " and "B   -223 -LEU -HD12" only  1.43 A apart
           %atoms "B   -225 -ASN -HN  " and "B   -225 -ASN -HD21" only  1.37 A apart
           %atoms "B   -246 -PHE -HE2 " and "B   -248 -HIS -HD1 " only  1.47 A apart
           %atoms "B   -337 -VAL -O   " and "B   -340 -ASP -HN  " only  1.42 A apart
           %atoms "C   -13  -DG  -H2''" and "C   -14  -DT  -H5' " only  1.31 A apart
           %atoms "C   -15  -DA  -H2' " and "C   -16  -DT  -H73 " only  1.48 A apart
           %atoms "C   -18  -DA  -H2''" and "C   -19  -DA  -H8  " only  1.46 A apart
           %atoms "C   -19  -DA  -H2' " and "C   -20  -DA  -H8  " only  1.50 A apart
           %atoms "C   -25  -DG  -H1  " and "D   -32  -DC  -H42 " only  1.27 A apart
           %atoms "D   -31  -DA  -H2''" and "D   -32  -DC  -H5' " only  1.44 A apart
           %atoms "D   -31  -DA  -H2''" and "D   -32  -DC  -H5''" only  1.38 A apart
           %atoms "D   -34  -DA  -H2''" and "D   -35  -DC  -H5''" only  1.34 A apart
           %atoms "D   -42  -DT  -H5''" and "D   -42  -DT  -H6  " only  1.16 A apart
           %atoms "D   -43  -DA  -H2''" and "D   -44  -DC  -H5''" only  1.18 A apart
           %atoms "D   -45  -DT  -H5' " and "D   -45  -DT  -H6  " only  1.34 A apart
           %atoms "D   -46  -DT  -H2''" and "D   -47  -DG  -H5' " only&

          (Message over 64 KB, truncated)
        • Ed Pozharski
          ... model_anneal_3HOS_X.pdb where X=1-10. Check your output folder. This is a concern though %CNSsolve error encountered: File model_anneal_3HOS_1_traj.crd
          Message 4 of 6 , May 17, 2012
          View Source
          • 0 Attachment
            On Thu, 2012-05-17 at 21:45 +0200, Jeanne Cambefort wrote:
            > Otherwise tihs is my log file :
            >

            >From which you can see that the snapshots were saved in files named
            model_anneal_3HOS_X.pdb where X=1-10. Check your output folder.

            This is a concern though

            %CNSsolve> error encountered: File model_anneal_3HOS_1_traj.crd was
            not open.
            (CNS is in mode: SET ABORT=NORMal END)


            Maybe you are trying to write into a read-only folder?

            --
            "Hurry up before we all come back to our senses!"
            Julian, King of Lemurs
          • Jeanne Cambefort
            ... Well all the snapshots seem to be created at the same time, and they seem to be very similar. But they are created. I did not see this error. ... Of course
            Message 5 of 6 , May 17, 2012
            View Source
            • 0 Attachment
              >From which you can see that the snapshots were saved in files named
              > model_anneal_3HOS_X.pdb where X=1-10. Check your output folder.

              Well all the snapshots seem to be created at the same time, and they seem
              to be very similar. But they are created. I did not see this error.
              > %CNSsolve> error encountered: File model_anneal_3HOS_1_traj.crd was
              > not open.
              > (CNS is in mode: SET ABORT=NORMal END)

              > Maybe you are trying to write into a read-only folder?
              Of course not. Is it the parameter files or the molecule file?
              I'm not in the lab, I cannot run CNSsolve until Monday, I'm sorry.
              I thank you.
              Jeanne


            • Ed Pozharski
              ... That s OK - snapshots are indeed created at the end of each trial, all at the same time. As for the snapshots being very similar - they are only separated
              Message 6 of 6 , May 17, 2012
              View Source
              • 0 Attachment
                On Thu, 2012-05-17 at 22:10 +0100, Jeanne Cambefort wrote:
                > Well all the snapshots seem to be created at the same time, and they
                > seem to be very similar. But they are created.

                That's OK - snapshots are indeed created at the end of each trial, all
                at the same time.

                As for the snapshots being very similar - they are only separated by
                50fs - how different you expect them to be?
              Your message has been successfully submitted and would be delivered to recipients shortly.