Re: [gmx-users] Residue 'DEF' not found in residue topology database

Justin A. Lemkul Thu, 24 Feb 2011 03:36:31 -0800


Emine Deniz Tekin wrote:


Hi Justin,


Thank you for your reply.


Before I contacted you and do what you suggested , I did the following way:


  1)      Firstly, I created the lipopetide (12 Carbon atoms (tail) +
  Val-Val-Ala-Gly-Glu-Arg-Gly-Asp) using ChemDraw and saved as a PDB.


  2)      Then, I pasted my pdb file to the The Dundee PRODRG2.5 Server
  (beta) and I got conf.gro and topol.top files.

This will give you very bad parameters. Seehttp://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips and the paperlinked therein.


  3)      After completing some of the missing information by hand at
  the topology file (e.g  #include "gromos53a6.ff/forcefield.itp"..),
  started the simulation for 10 ns.


  Simulation went through without an apparent error. But I saw that when
  I watch the trajectory at Visual Molecular Dynamics (VMD), some bonds
  seem much longer than they should be.


  What could be the reason for this? I wonder  if something ‘s wrong in
  the above process.

VMD guesses where bonds should be based on a heuristic algorithm. It could alsobe a periodicity effect:


http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin

Thank you in advance,

Deniz

On Wed, Feb 23, 2011 at 3:57 PM, Justin A. Lemkul <jalem...@vt.edu<mailto:jalem...@vt.edu>> wrote:




    Emine Deniz Tekin wrote:


        Hi gromacs users,


        I am using the gromacs 4.5.3 version. I created a lipopetide
        which consist of 12 Carbon atoms (tail) connected to
        Val-Val-Ala-Gly-Glu-Arg-Gly-Asp (residues) using ARGUSLAB and I
        saved it as a pdb file.

        Then, when I used the following command in gromacs:

         pdb2gmx   –f    lipopepArgus.pdb    (GROMOS96 45a3 force
        field&spc type water model)

         I got the following error message:

         Fatal error:

        Residue 'DEF' not found in residue topology database

        For more information and tips for troubleshooting, please check
        the GROMACS

        website at http://www.gromacs.org/Documentation/Errors

As far as I could understand, there is no problem with the

        residues  but  there is a problem with the atoms in the tail (12
        Carbon atoms, 23 Hydrogen atoms and an Oxygen atom, actually it
        is called a lauroic acid). These atoms are defined as DEF.  I
        thought  I should  rename the pdb to the expected name given in
        the .rtp file of  the 45a3 force field for my lipopeptide. But I
        could not find a parameterization for the  lauroic acid. In this
        case, what shoul I do?


        At the
         
http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks
        page, I found;


        *Abbrev.*

        *Source*

*2*

        *Full Name*

        *Formula*

        *Specifics*

        LAU

        fa.itp

        lauroic acid

        C_11 H_23 COOH

Does using fa.itp file solve my problem? If yes, where can I get

        this file?



    This topology is from the deprecated Gromos87 (hacked) force field
    called ffgmx.  Don't use it.  The reasons are described in the
    manual.  What's more, you can't use a standalone topology if your
    molecule is covalently linked to a peptide.  You can't have bonds
    between different [moleculetypes] (i.e. between topologies) in Gromacs.

    The proper procedure is to parameterize the lauroic acid:

    http://www.gromacs.org/Documentation/How-tos/Parameterization

    or obtain compatible parameters from elsewhere and implement them in
    your chosen force field:

    
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

    You could use Berger lipid parameters for the lauroic acid moiety,
    you'll just have to add this residue to the force field.  The
    membrane protein tutorial I wrote will walk you through how to
    modify the force field properly.

    http://www.gromacs.org/Documentation/Tutorials#Membrane_Simulations

    -Justin


        I would be so glad if you can help me solve this problem.
        Thank you in advance,

        Deniz

--========================================


    Justin A. Lemkul
    Ph.D. Candidate
    ICTAS Doctoral Scholar
    MILES-IGERT Trainee
    Department of Biochemistry
    Virginia Tech
    Blacksburg, VA
    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

    ========================================

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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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Re: [gmx-users] Residue 'DEF' not found in residue topology database

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