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

[Justin A. Lemkul]

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.  See 
http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips and the paper 
linked 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 also 
be 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 <jalemkul at vt.edu 
> <mailto:jalemkul at 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
> 
>                
> 
>         O
> 
>                
> 
>         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

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