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MAXJNT variable problem

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  • David Aragao
    Hello to all, I have a problem when running cns_solve on a anneal.inp file (defaults) Program version= 1.1 File version= 1.1 SELRPN: 0 atoms have been
    Message 1 of 4 , May 31, 2002
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      Hello to all,

      I have a problem when running cns_solve on a anneal.inp file (defaults)

      Program version= 1.1 File version= 1.1
      SELRPN: 0 atoms have been selected out of 4231
      -------------------------- Torsion Topology
      -----------------------------------
      ERROR: A group has too many joints.
      Please increase MAXJNT and re-run.

      %TORSION:TOPOLOGY error encountered: Fatal Topology Error
      (CNS is in mode: SET ABORT=NORMal END)
      *****************************************************
      ABORT mode will terminate program execution.
      *****************************************************
      Program will stop immediately.

      Should I change
      /usr/local/cns_solve_1.1/source/dtorsion_top.f: MAXJNT=7
      and recompile ?

      What for is this variable used ?

      Best regards,

      David

      --
      David Aragao
      http://david.aragao.name

      "For every complex problem there is an answer that is clear, simple,
      and wrong."
      - H. L. Mencken (1880-1956)
    • virtual_train
      Hello to all, I have a problem when running cns_solve on a anneal.inp file (defaults) Program version= 1.1 File version= 1.1 SELRPN: 0 atoms have been
      Message 2 of 4 , May 31, 2002
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        Hello to all,

        I have a problem when running cns_solve on a anneal.inp file
        (defaults)

        Program version= 1.1 File version= 1.1
        SELRPN: 0 atoms have been selected out of 4231
        -------------------------- Torsion Topology
        -----------------------------------
        ERROR: A group has too many joints.
        Please increase MAXJNT and re-run.

        %TORSION:TOPOLOGY error encountered: Fatal Topology Error
        (CNS is in mode: SET ABORT=NORMal END)
        *****************************************************
        ABORT mode will terminate program execution.
        *****************************************************
        Program will stop immediately.

        Should I change
        /usr/local/cns_solve_1.1/source/dtorsion_top.f: MAXJNT=7
        and recompile ?

        What for is this variable used ?

        Best regards,

        David

        P.S: I have seen in the FAQ but didn't quite answer how and why...

        --
        David Aragao
        http://david.aragao.name
        daragao@... (work)
        david@... (home)
        "For every complex problem there is an answer that is clear, simple,
        and wrong."
        - H. L. Mencken (1880-1956)
      • Luke Rice
        What Evan said. (Hi Evan, by the way). One additional comment - MAXJNT refers to the maximum number of connections one rigid group can have to others. The
        Message 3 of 4 , Jun 3, 2002
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          What Evan said. (Hi Evan, by the way).

          One additional comment - MAXJNT refers to the maximum number of
          connections one rigid group can have to others. The fact that you need
          more than seven connections indicates one of two things (and perhaps
          both):

          1. You have some semi-complicated covalent geometry
          2. You force constants for the torsions in said geometry are below the
          threshold for what gets kept rigid, and hence you are allowing some
          torsional degrees of freedom you may or may not want to.

          The simple way to make the problem go away is to increase MAXJNT, just
          pay attention to what's going on with the geometry of the ligand I
          assume you have.

          Luke


          On Fri, 2002-05-31 at 09:19, David Aragao wrote:
          > Hello to all,
          >
          > I have a problem when running cns_solve on a anneal.inp file (defaults)
          >
          > Program version= 1.1 File version= 1.1
          > SELRPN: 0 atoms have been selected out of 4231
          > -------------------------- Torsion Topology
          > -----------------------------------
          > ERROR: A group has too many joints.
          > Please increase MAXJNT and re-run.
          >
          > %TORSION:TOPOLOGY error encountered: Fatal Topology Error
          > (CNS is in mode: SET ABORT=NORMal END)
          > *****************************************************
          > ABORT mode will terminate program execution.
          > *****************************************************
          > Program will stop immediately.
          >
          > Should I change
          > /usr/local/cns_solve_1.1/source/dtorsion_top.f: MAXJNT=7
          > and recompile ?
          >
          > What for is this variable used ?
          >
          > Best regards,
          >
          > David
          >
          > --
          > David Aragao
          > http://david.aragao.name
          >
          > "For every complex problem there is an answer that is clear, simple,
          > and wrong."
          > - H. L. Mencken (1880-1956)
          >
          >
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          > Posting is only allowed for members of this list.
          > To unsubscribe from this group, send an email to:
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          >
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          >
          >
        • Evan Stein
          According to the FAQ, MAXJNT indicates the maximum number of atoms that another atom may be bonded to when CNS sets up the topology for Torsion Angle Dynamics.
          Message 4 of 4 , Jun 3, 2002
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            According to the FAQ, MAXJNT indicates the maximum number of atoms that
            another atom may be bonded to when CNS sets up the topology for Torsion
            Angle Dynamics. More precisely, I believe this is maxbond and maxjoint is
            the maximum number of branch points per constrained group. These parameters
            are related. By default, MAXJNT is set to 7.

            Is there an atom in your molecule that should be bonded to more than seven
            other atoms? If not, there is a problem with your topology set-up and you
            need to go back and look at the file you use to generate your MTF
            (structure-file).

            If you expect to have atoms bonded to more than 7 atoms, you can increase
            MAXJNT in the script by just editing the anneal.inp script to include a
            torsion_maxjoint value. The changes I made were around line 280 and around
            line 825 in the anneal.inp script.

            (LINE ~280)
            {* maximum number of bonds to an atom *}
            {===>} torsion_maxbond=6;
            {* NEWLINE maximum number of branch points per constrained group *}
            { NEWLINE ===>} torsion_maxjoint=9;

            (LINE ~825)
            maxbond=&torsion_maxbond
            { NEWLINE } maxjoint=&torsion_maxjoint

            --
            Evan Stein
            Structural Biology Program
            Skirball Institute / NYU School of Medicine
            540 First Avenue Lab 3-4
            New York, NY 10016

            phone: (212) 263-8968
            fax: (212) 263-8951
            email: stein@...
            URL: http://saturn.med.nyu.edu/~stein


            > From: David Aragao <daragao@...>
            > Organization: ITQB - Oeiras
            > Reply-To: daragao@...
            > Date: Fri, 31 May 2002 15:19:02 +0100
            > To: cnsbb@yahoogroups.com
            > Subject: [cnsbb] MAXJNT variable problem
            >
            > Hello to all,
            >
            > I have a problem when running cns_solve on a anneal.inp file (defaults)
            >
            > Program version= 1.1 File version= 1.1
            > SELRPN: 0 atoms have been selected out of 4231
            > -------------------------- Torsion Topology
            > -----------------------------------
            > ERROR: A group has too many joints.
            > Please increase MAXJNT and re-run.
            >
            > %TORSION:TOPOLOGY error encountered: Fatal Topology Error
            > (CNS is in mode: SET ABORT=NORMal END)
            > *****************************************************
            > ABORT mode will terminate program execution.
            > *****************************************************
            > Program will stop immediately.
            >
            > Should I change
            > /usr/local/cns_solve_1.1/source/dtorsion_top.f: MAXJNT=7
            > and recompile ?
            >
            > What for is this variable used ?
            >
            > Best regards,
            >
            > David
            >
            > --
            > David Aragao
            > http://david.aragao.name
            >
            > "For every complex problem there is an answer that is clear, simple,
            > and wrong."
            > - H. L. Mencken (1880-1956)
            >
            >
            > --------------------------------------------------------
            > List information at http://groups.yahoo.com/group/cnsbb.
            > Posting is only allowed for members of this list.
            > To unsubscribe from this group, send an email to:
            > cnsbb-unsubscribe@yahoogroups.com.
            >
            >
            >
            > Your use of Yahoo! Groups is subject to http://docs.yahoo.com/info/terms/
            >
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