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Error from translation.inp

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  • Debajyoti Dutta
    Hi All, I am executing translation.inp for a 2.0A data. I have sucessfully got the cross rotation output peaks. But when trying to run the translation.inp I am
    Message 1 of 4 , Jul 1, 2008
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      Hi All,

      I am executing translation.inp for a 2.0A data. I have sucessfully got the cross rotation output peaks. But when trying to run the translation.inp I am getting the following errors

      RIGID: main coordinates set to best minimum
       %NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%%
        ATOM: SEGId="O   ",  RESId="338 ",  NAME="S   ",  CHEMical="SUF "
       %NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%%
        ATOM: SEGId="O   ",  RESId="338 ",  NAME="O1  ",  CHEMical="OUF "

      %NBUPDA error encountered: program will be aborted.
         (CNS is in mode: SET ABORT=NORMal END)
       *****************************************************
       ABORT mode will terminate program execution.
       *****************************************************
       Program will stop immediately.

      Does I have to change the model.pdb (all the residues are there: generated by generate_easy, and contain ligands and waters) file or I have to fix or limit some bond parameters. I have set the resolution limits 30A to 2.0A for both cross rotation and translation inp.

      Please help me as I am very new CNS user.

      Thank you for your suggestions in advance.

      Yours Sincerely
      Debajyoti Dutta
       


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    • Gerard DVD Kleywegt
      well, you could fix the *symptom* by defining top/par for the ligand(s), but for molecular replacement calculations you should really remove all ligands and
      Message 2 of 4 , Jul 2, 2008
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        well, you could fix the *symptom* by defining top/par for the ligand(s), but
        for molecular replacement calculations you should really remove all ligands
        and waters. count yourself lucky: this is one of those rare cases in life
        where fixing the problem is less work than fixing the symptoms ;-)

        --gerard

        ******************************************************************
        Gerard J. Kleywegt
        [Research Fellow of the Royal Swedish Academy of Sciences]
        Dept. of Cell & Molecular Biology University of Uppsala
        Biomedical Centre Box 596
        SE-751 24 Uppsala SWEDEN

        http://xray.bmc.uu.se/gerard/ mailto:gerard@...
        ******************************************************************
        The opinions in this message are fictional. Any similarity
        to actual opinions, living or dead, is purely coincidental.
        ******************************************************************
      • Debajyoti Dutta
        Hi again, Thank you all for your suggestions. I am very sorry for my incomplete mail. Actually translation.inp is giving error for may atoms I have taken only
        Message 3 of 4 , Jul 2, 2008
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          Hi again,

          Thank you all for your suggestions. I am very sorry for my incomplete mail. Actually translation.inp is giving error for may atoms I have taken only two to save space as probably all errors are related to same reason.

          Initially I had prepared my model with generate_easy.inp but unfortunately  the input PDB contain ligans and waters. But before that I prepared my model with generate.inp giving
          inputs of ligans, waters and model differently. That time also translation.inp is also giving
          the same error.

          But I don't know how to prepare the ligand parameter file
          CNS_TOPPAR:protein_rep.param). Please guide me.

          Yous Sincerely
          Debajyoti




          --- On Wed, 2/7/08, Ed Pozharski <epozh001@...> wrote:
          From: Ed Pozharski <epozh001@...>
          Subject: Re: [cnsbb] Error from translation.inp
          To: molbiol349@...
          Date: Wednesday, 2 July, 2008, 6:35 PM

          Sounds like you don't have the parameter file for the ligand.  Another
          strange thing is that you seem to have two atoms from the residue with
          the same segid (O) and resid (338) but different resname (SUF and OUF).

          On Wed, 2008-07-02 at 10:54 +0530, Debajyoti Dutta wrote:
          >
          > Hi All,
          >
          > I am executing translation.inp for a 2.0A data. I have sucessfully got
          > the cross rotation output peaks. But when trying to run the
          > translation.inp I am getting the following errors
          >
          > RIGID: main coordinates set to best minimum
          > %NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%%
          > ATOM: SEGId="O ", RESId="338 ", NAME="S
          ", CHEMical="SUF "
          > %NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%%
          > ATOM: SEGId="O ", RESId="338 ", NAME="O1
          ", CHEMical="OUF "
          >
          > %NBUPDA error encountered: program will be aborted.
          > (CNS is in mode: SET ABORT=NORMal END)
          > *****************************************************
          > ABORT mode will terminate program execution.
          > *****************************************************
          > Program will stop immediately.
          >
          > Does I have to change the model.pdb (all the residues are there:
          > generated by generate_easy, and contain ligands and waters) file or I
          > have to fix or limit some bond parameters. I have set the resolution
          > limits 30A to 2.0A for both cross rotation and translation inp.
          >
          > Please help me as I am very new CNS user.
          >
          > Thank you for your suggestions in advance.
          >
          > Yours Sincerely
          > Debajyoti Dutta
          >
          >
          >
          >
          >
          >
          > ______________________________________________________________________
          > Best Jokes, Best Friends, Best Food. Get all this and more on Best of
          > Yahoo! Groups.
          >
          >
          >
          --
          Edwin Pozharski, PhD, Assistant Professor
          University of Maryland, Baltimore
          ----------------------------------------------
          When the Way is forgotten duty and justice appear;
          Then knowledge and wisdom are born along with hypocrisy.
          When harmonious relationships dissolve then respect and devotion arise;
          When a nation falls to chaos then loyalty and patriotism are born.
          ------------------------------ / Lao Tse /


          Explore your hobbies and interests. Click here to begin.
        • Debajyoti Dutta
          Hi all, Thank you for all replies, suggestions. All helped me a lot. Sincerely Debajyoti ... From: Ed Pozharski Subject: Re: [cnsbb]
          Message 4 of 4 , Jul 3, 2008
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            Hi all,

            Thank you for all replies, suggestions. All helped me a lot.

            Sincerely
            Debajyoti


            --- On Wed, 2/7/08, Ed Pozharski <epozh001@...> wrote:
            From: Ed Pozharski <epozh001@...>
            Subject: Re: [cnsbb] Error from translation.inp
            To: molbiol349@...
            Date: Wednesday, 2 July, 2008, 10:52 PM

            Why don't you remove ligand and waters from the pdb-file?  In fact, you
            MUST remove thme for molecular replacement.

            Topology/parameter files can be generated manually (see CNS tutorial),
            using xplo2d (Uppsala Software Factory) or PRODRG server.

            On Wed, 2008-07-02 at 21:18 +0530, Debajyoti Dutta wrote:
            >
            > Hi again,
            >
            > Thank you all for your suggestions. I am very sorry for my incomplete
            > mail. Actually translation.inp is giving error for may atoms I have
            > taken only two to save space as probably all errors are related to
            > same reason.
            >
            > Initially I had prepared my model with generate_easy.inp but
            > unfortunately the input PDB contain ligans and waters. But before
            > that I prepared my model with generate.inp giving
            > inputs of ligans, waters and model differently. That time also
            > translation.inp is also giving
            > the same error.
            >
            > But I don't know how to prepare the ligand parameter file
            > CNS_TOPPAR:protein_rep.param). Please guide me.
            >
            > Yous Sincerely
            > Debajyoti
            >
            >
            >
            >
            > --- On Wed, 2/7/08, Ed Pozharski <epozh001@...> wrote:
            > From: Ed Pozharski <epozh001@...>
            > Subject: Re: [cnsbb] Error from translation.inp
            > To: molbiol349@...
            > Date: Wednesday, 2 July, 2008, 6:35 PM
            >
            > Sounds like you don't have the parameter file for the ligand.
            Another
            > strange thing is that you seem to have two atoms from the residue
            with
            > the same segid (O) and resid (338) but different resname (SUF and
            OUF).
            >
            > On Wed, 2008-07-02 at 10:54 +0530, Debajyoti Dutta wrote:
            > >
            > > Hi All,
            > >
            > > I am executing translation.inp for a 2.0A data. I have
            sucessfully got
            > > the cross rotation output peaks. But when trying to run the
            > > translation.inp I am getting the following errors
            > >
            > > RIGID: main coordinates set to best minimum
            > > %NBUPDA-ERR: missing nonbonded Lennard-Jones parameters
            %%%%%%%
            > > ATOM: SEGId="O ", RESId="338 ",
            NAME="S
            > ", CHEMical="SUF "
            > >
            > %NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%%
            > > ATOM: SEGId="O ", RESId="338 ",
            NAME="O1
            > ", CHEMical="OUF "
            > >
            > > %NBUPDA error encountered: program will be aborted.
            > > (CNS is in mode: SET ABORT=NORMal END)
            > > *****************************************************
            > > ABORT mode will terminate program execution.
            > > *****************************************************
            > > Program will stop immediately.
            > >
            > > Does I have to change the model.pdb (all the residues are
            there:
            > > generated by generate_easy, and contain ligands and waters)
            file or I
            > > have to fix or limit some bond parameters. I have set the
            resolution
            > > limits 30A to 2.0A for both cross rotation and translation
            inp.
            > >
            > > Please help me as I am very new CNS user.
            > >
            > > Thank you for your suggestions in advance.
            > >
            > > Yours Sincerely
            > > Debajyoti
            > Dutta
            > >
            > >
            > >
            > >
            > >
            > >
            > >
            ______________________________________________________________________
            > > Best Jokes, Best Friends, Best Food. Get all this and more on
            Best of
            > > Yahoo! Groups.
            > >
            > >
            > >
            > --
            > Edwin Pozharski, PhD, Assistant Professor
            > University of Maryland, Baltimore
            > ----------------------------------------------
            > When the Way is forgotten duty and justice appear;
            > Then knowledge and wisdom are born along with hypocrisy.
            > When harmonious relationships dissolve then
            > respect and devotion arise;
            > When a nation falls to chaos then loyalty and patriotism are born.
            > ------------------------------ / Lao Tse /
            >
            >
            > ______________________________________________________________________
            > Explore your hobbies and interests. Click here to begin.
            --
            Edwin Pozharski, PhD, Assistant Professor
            University of Maryland, Baltimore
            ----------------------------------------------
            When the Way is forgotten duty and justice appear;
            Then knowledge and wisdom are born along with hypocrisy.
            When harmonious relationships dissolve then respect and devotion arise;
            When a nation falls to chaos then loyalty and patriotism are born.
            ------------------------------ / Lao Tse /


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