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water_pick.inp problem

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  • drhmcdonald
    Hi, I am having trouble running water_pick.inp on my linux machine. In the past, I have had no trouble running the water_pick.inp on an SGI machine. This is a
    Message 1 of 4 , Feb 1, 2005
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      Hi,

      I am having trouble running water_pick.inp on my linux machine. In the
      past, I have had no trouble running the water_pick.inp on an SGI
      machine. This is a decent data set (Res = 1.8 A, R= 24.84, Rfree =
      28.57). Any thoughts are greatly appreciated. Below is the error message.

      Thanks,
      Heather

      SELRPN> ( name O* or name N* ) ) saround &hmax ) ) )
      SELRPN: 0 atoms have been selected out of 4068
      DELETE> end
      SCRATC-warning: XRAY SCATter database erased.
      Status of internal molecular topology database:
      -> NATOM= 4068(MAXA= 40000) NBOND= 4136(MAXB=
      40000)
      -> NTHETA= 5561(MAXT= 80000) NGRP= 521(MAXGRP=
      40000)
      -> NPHI= 2621(MAXP= 80000) NIMPHI= 1667(MAXIMP=
      40000)
      -> NNB= 0(MAXNB= 40000)
      CNSsolve> end if
      CNSsolve>
      CNSsolve> parameter nbonds special_position=&special_dist end end
      %PARRDR-ERROR: duplication of bond HT HT
      %PARRDR-ERROR: duplication of bond HT OT
      %PARRDR-ERROR: duplication of angle HT OT HT
      %PARRDR-ERROR: duplication of nonbonded entry HT
      %PARRDR-ERROR: duplication of nonbonded entry OT
      CNSsolve>
      CNSsolve> if ( &peak_special = false ) then
      NEXTCD: condition evaluated as true
      CNSsolve> xray
      XRAY> @@CNS_XRAYLIB:scatter.lib
      ASSFIL: file
      /usr/local/progs/cns_solve_1.1/libraries/xray/scatter.lib opened.
      XRAY>! file libraries/xray/scatter.lib
      XRAY>! Atomic scattering factors without anomalous contribution
      XRAY>! Library for CNS
      XRAY>
      XRAY>! Authors: Paul Adams, Joe Jaeger, and Axel T. Brunger
      XRAY>
      XRAY>!BEWARE:
      XRAY>!(1) element Cf (Californium) has to be referred to as Cff
      XRAY>!(2) element Sm (Samarium) has to be referred to as Smm
      XRAY>!(3) element Np (Neptunium) has to be referred to as Npp
      XRAY>!(3) types of elements with ionic state (i.e., +/-)
      specifications have
      XRAY>! to be put in double quotes in selection statements.
      XRAY>
      XRAY>set message ? end
      MESSage=NORM
      XRAY>evaluate ($message_old_sclib=$result)
      EVALUATE: symbol $MESSAGE_OLD_SCLIB set to "NORM" (string)
      XRAY>set echo ? end
      ECHO=TRUE {ON}
      XRAY>evaluate ($echo_old_sclib=$result)
      EVALUATE: symbol $ECHO_OLD_SCLIB set to TRUE (logical)
      XRAY>set echo=off message=off end
      Program version= 1.1 File version= 1.1
      XRAY> special selection=( segid PEAK ) to=rmsd end
      SELRPN: 0 atoms have been selected out of 4068
      %XSPEcial-ERR: zero atoms selected.
      %XSPEcial error encountered: zero atoms selected.
      (CNS is in mode: SET ABORT=NORMal END)
      *****************************************************
    • Pilar Saiz Vela
      Dear xplor/cns users, is there an easy way of putting a peptide inside a water box and perform with that system a molecular dynamics calculation? (as a final
      Message 2 of 4 , Feb 7, 2005
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        Dear xplor/cns users,

        is there an easy way of putting a peptide inside a water box and perform
        with that system a molecular dynamics calculation? (as a final
        refinement step)

        I will really appreciate your help.
        PILAR

        El mar, 01 de 02 de 2005 a las 17:37, drhmcdonald escribió:
        >
        > Hi,
        >
        > I am having trouble running water_pick.inp on my linux machine. In the
        > past, I have had no trouble running the water_pick.inp on an SGI
        > machine. This is a decent data set (Res = 1.8 A, R= 24.84, Rfree =
        > 28.57). Any thoughts are greatly appreciated. Below is the error message.
        >
        > Thanks,
        > Heather
        >
        > SELRPN> ( name O* or name N* ) ) saround &hmax ) ) )
        > SELRPN: 0 atoms have been selected out of 4068
        > DELETE> end
        > SCRATC-warning: XRAY SCATter database erased.
        > Status of internal molecular topology database:
        > -> NATOM= 4068(MAXA= 40000) NBOND= 4136(MAXB=
        > 40000)
        > -> NTHETA= 5561(MAXT= 80000) NGRP= 521(MAXGRP=
        > 40000)
        > -> NPHI= 2621(MAXP= 80000) NIMPHI= 1667(MAXIMP=
        > 40000)
        > -> NNB= 0(MAXNB= 40000)
        > CNSsolve> end if
        > CNSsolve>
        > CNSsolve> parameter nbonds special_position=&special_dist end end
        > %PARRDR-ERROR: duplication of bond HT HT
        > %PARRDR-ERROR: duplication of bond HT OT
        > %PARRDR-ERROR: duplication of angle HT OT HT
        > %PARRDR-ERROR: duplication of nonbonded entry HT
        > %PARRDR-ERROR: duplication of nonbonded entry OT
        > CNSsolve>
        > CNSsolve> if ( &peak_special = false ) then
        > NEXTCD: condition evaluated as true
        > CNSsolve> xray
        > XRAY> @@CNS_XRAYLIB:scatter.lib
        > ASSFIL: file
        > /usr/local/progs/cns_solve_1.1/libraries/xray/scatter.lib opened.
        > XRAY>! file libraries/xray/scatter.lib
        > XRAY>! Atomic scattering factors without anomalous contribution
        > XRAY>! Library for CNS
        > XRAY>
        > XRAY>! Authors: Paul Adams, Joe Jaeger, and Axel T. Brunger
        > XRAY>
        > XRAY>!BEWARE:
        > XRAY>!(1) element Cf (Californium) has to be referred to as Cff
        > XRAY>!(2) element Sm (Samarium) has to be referred to as Smm
        > XRAY>!(3) element Np (Neptunium) has to be referred to as Npp
        > XRAY>!(3) types of elements with ionic state (i.e., +/-)
        > specifications have
        > XRAY>! to be put in double quotes in selection statements.
        > XRAY>
        > XRAY>set message ? end
        > MESSage=NORM
        > XRAY>evaluate ($message_old_sclib=$result)
        > EVALUATE: symbol $MESSAGE_OLD_SCLIB set to "NORM" (string)
        > XRAY>set echo ? end
        > ECHO=TRUE {ON}
        > XRAY>evaluate ($echo_old_sclib=$result)
        > EVALUATE: symbol $ECHO_OLD_SCLIB set to TRUE (logical)
        > XRAY>set echo=off message=off end
        > Program version= 1.1 File version= 1.1
        > XRAY> special selection=( segid PEAK ) to=rmsd end
        > SELRPN: 0 atoms have been selected out of 4068
        > %XSPEcial-ERR: zero atoms selected.
        > %XSPEcial error encountered: zero atoms selected.
        > (CNS is in mode: SET ABORT=NORMal END)
        > *****************************************************
        >
        >
        >
        >
        >
        >
        > --------------------------------------------------------
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      • htc2001_cn
        Hi all! I encountered the same problem. CNS 1.1 under windows XP works fine with water_pick, while RedHat Linux ES3 had trouble when dealing with the same
        Message 3 of 4 , Mar 28, 2005
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          Hi all!

          I encountered the same problem. CNS 1.1 under windows XP works fine
          with water_pick, while RedHat Linux ES3 had trouble when dealing with
          the same data.

          Could anyone give me some instructions?

          Thanks in advance!


          --- In cnsbb@yahoogroups.com, "drhmcdonald" <drhmcdonald@y...> wrote:
          >
          >
          > Hi,
          >
          > I am having trouble running water_pick.inp on my linux machine. In
          the
          > past, I have had no trouble running the water_pick.inp on an SGI
          > machine. This is a decent data set (Res = 1.8 A, R= 24.84, Rfree =
          > 28.57). Any thoughts are greatly appreciated. Below is the error
          message.
          >
          > Thanks,
          > Heather
          >
          > SELRPN> ( name O* or name N* ) ) saround &hmax
          ) ) )
          > SELRPN: 0 atoms have been selected out of 4068
          > DELETE> end
          > SCRATC-warning: XRAY SCATter database erased.
          > Status of internal molecular topology database:
          > -> NATOM= 4068(MAXA= 40000) NBOND= 4136(MAXB=

          > 40000)
          > -> NTHETA= 5561(MAXT= 80000) NGRP= 521(MAXGRP=

          > 40000)
          > -> NPHI= 2621(MAXP= 80000) NIMPHI= 1667(MAXIMP=

          > 40000)
          > -> NNB= 0(MAXNB= 40000)
          > CNSsolve> end if
          > CNSsolve>
          > CNSsolve> parameter nbonds special_position=&special_dist end end
          > %PARRDR-ERROR: duplication of bond HT HT
          > %PARRDR-ERROR: duplication of bond HT OT
          > %PARRDR-ERROR: duplication of angle HT OT HT
          > %PARRDR-ERROR: duplication of nonbonded entry HT
          > %PARRDR-ERROR: duplication of nonbonded entry OT
          > CNSsolve>
          > CNSsolve> if ( &peak_special = false ) then
          > NEXTCD: condition evaluated as true
          > CNSsolve> xray
          > XRAY> @@CNS_XRAYLIB:scatter.lib
          > ASSFIL: file
          > /usr/local/progs/cns_solve_1.1/libraries/xray/scatter.lib opened.
          > XRAY>! file libraries/xray/scatter.lib
          > XRAY>! Atomic scattering factors without anomalous contribution
          > XRAY>! Library for CNS
          > XRAY>
          > XRAY>! Authors: Paul Adams, Joe Jaeger, and Axel T. Brunger
          > XRAY>
          > XRAY>!BEWARE:
          > XRAY>!(1) element Cf (Californium) has to be referred to as Cff
          > XRAY>!(2) element Sm (Samarium) has to be referred to as Smm
          > XRAY>!(3) element Np (Neptunium) has to be referred to as Npp
          > XRAY>!(3) types of elements with ionic state (i.e., +/-)
          > specifications have
          > XRAY>! to be put in double quotes in selection statements.
          > XRAY>
          > XRAY>set message ? end
          > MESSage=NORM
          > XRAY>evaluate ($message_old_sclib=$result)
          > EVALUATE: symbol $MESSAGE_OLD_SCLIB set to "NORM" (string)
          > XRAY>set echo ? end
          > ECHO=TRUE {ON}
          > XRAY>evaluate ($echo_old_sclib=$result)
          > EVALUATE: symbol $ECHO_OLD_SCLIB set to TRUE (logical)
          > XRAY>set echo=off message=off end
          > Program version= 1.1 File version= 1.1
          > XRAY> special selection=( segid PEAK ) to=rmsd end
          > SELRPN: 0 atoms have been selected out of 4068
          > %XSPEcial-ERR: zero atoms selected.
          > %XSPEcial error encountered: zero atoms selected.
          > (CNS is in mode: SET ABORT=NORMal END)
          > *****************************************************
        • Mark A. White
          Hi, The problem may be one which Joe Krahn found earlier, memory allocation under Linux. Here is his fix for the problem, which was posted to the CCP4
          Message 4 of 4 , Mar 30, 2005
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            Hi,

            The problem may be one which Joe Krahn found earlier,  memory allocation under Linux.  Here is his fix for the problem, which was posted to the CCP4 bulletin board.  You will need to recompile CNS after fixing the code.


            **  For details on how to be removed from this list visit the  ***
            ***          CCP4 home page http://www.ccp4.ac.uk         ***

            Many F77 programs access memory from C malloc() via
            an out-of-bounds index to a HEAP array. It seems that
            malloc() used to always generate a positive array index
            in Linux (and presumably other OSes) but malloc() in
            Fedora and Enterprise Linux most often gives a negative
            array index.

            This exposes a bug in CNS, as well as some of my own code.
            It might affect other programs using C malloc() from F77.

            The bug and fix in CNS is in xpeakpik.f, which results in
            never getting any peaks picked:

            *** 143,147 ****
                    DONE=.FALSE.
              C
            !       IF (MPACK.GT.0) THEN
              C
                    IF (.NOT.ERR.AND.HPRRHO(IFROM).EQ.0) THEN
            --- 143,147 ----
                    DONE=.FALSE.
              C
            !       IF (MPACK.NE.0) THEN
              C
                    IF (.NOT.ERR.AND.HPRRHO(IFROM).EQ.0) THEN

            The intent is to check if MPACK Heap memory is allocated,
            i.e. if MPACK==NULL, which worked only if the MPACK was positive.

            Joe Krahn


            htc2001_cn wrote:
            Hi all!
            
            I encountered the same problem. CNS 1.1 under windows XP works fine
            with water_pick, while RedHat Linux ES3 had trouble when dealing with
            the same data.
            
            Could anyone give me some instructions?
            
            Thanks in advance!
            
            
            --- In cnsbb@yahoogroups.com, "drhmcdonald" <drhmcdonald@y...> wrote:
              
            Hi,
            
            I am having trouble running water_pick.inp on my linux machine. In
                
            the
              
            past, I have had no trouble running the water_pick.inp on an SGI
            machine. This is a decent data set (Res = 1.8 A, R= 24.84, Rfree =
            28.57). Any thoughts are greatly appreciated. Below is the error
                
            message.
              
            Thanks,
            Heather
            
            SELRPN>                       ( name O* or name N* ) ) saround &hmax
                
            ) ) )
              
             SELRPN:      0 atoms have been selected out of   4068
             DELETE>   end
             SCRATC-warning: XRAY SCATter database erased.
             Status of internal molecular topology database:
             -> NATOM=       4068(MAXA=       40000)  NBOND=       4136(MAXB=  
                
             
              
              40000)
             -> NTHETA=      5561(MAXT=       80000)  NGRP=         521(MAXGRP=
                
             
              
              40000)
             -> NPHI=        2621(MAXP=       80000)  NIMPHI=      1667(MAXIMP=
                
             
              
              40000)
             -> NNB=            0(MAXNB=      40000)
             CNSsolve> end if
             CNSsolve>
             CNSsolve> parameter nbonds special_position=&special_dist end end
             %PARRDR-ERROR: duplication of bond HT   HT
             %PARRDR-ERROR: duplication of bond HT   OT
             %PARRDR-ERROR: duplication of angle HT   OT   HT
             %PARRDR-ERROR: duplication of nonbonded entry HT
             %PARRDR-ERROR: duplication of nonbonded entry OT
             CNSsolve>
             CNSsolve> if ( &peak_special = false ) then
             NEXTCD: condition evaluated as true
             CNSsolve>   xray
             XRAY>     @@CNS_XRAYLIB:scatter.lib
             ASSFIL: file
            /usr/local/progs/cns_solve_1.1/libraries/xray/scatter.lib opened.
             XRAY>! file libraries/xray/scatter.lib
             XRAY>! Atomic scattering factors without anomalous contribution
             XRAY>! Library for CNS
             XRAY>
             XRAY>! Authors: Paul Adams, Joe Jaeger, and Axel T. Brunger
             XRAY>
             XRAY>!BEWARE:
             XRAY>!(1) element Cf (Californium) has to be referred to as Cff
             XRAY>!(2) element Sm (Samarium) has to be referred to as Smm
             XRAY>!(3) element Np (Neptunium) has to be referred to as Npp
             XRAY>!(3) types of elements with ionic state (i.e., +/-)
            specifications have
             XRAY>!    to be put in double quotes in selection statements.
             XRAY>
             XRAY>set message ? end
             MESSage=NORM
             XRAY>evaluate ($message_old_sclib=$result)
             EVALUATE: symbol $MESSAGE_OLD_SCLIB set to "NORM" (string)
             XRAY>set echo ? end
             ECHO=TRUE {ON}
             XRAY>evaluate ($echo_old_sclib=$result)
             EVALUATE: symbol $ECHO_OLD_SCLIB set to TRUE (logical)
             XRAY>set echo=off message=off end
             Program version= 1.1 File version= 1.1
             XRAY>     special selection=( segid PEAK ) to=rmsd end
             SELRPN:      0 atoms have been selected out of   4068
             %XSPEcial-ERR: zero atoms selected.
             %XSPEcial error encountered: zero atoms selected.
               (CNS is in mode: SET ABORT=NORMal END)
             *****************************************************
                
            
            
            
            
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            -- 
            
            Best Regards,
            
            Mark
            
            -_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_
            Mark A. White, Ph.D.                                Tel: 
            Sealy Center for Structural Biology                 (409) 747-4747
            Dept. of Human Biological Chemistry & Genetics      Fax: 
            Basic Science Building, Room 660C                   (409) 747-4745
            University of Texas Medical Branch                  email:
            Galveston, TX 77555-0647              mailto://white@...
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