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

[Justin A. Lemkul]

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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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