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

[Emine Deniz Tekin]

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_Blockspage,
I found;


  *Abbrev.*

*Source*

*2*

*Full Name*

*Formula*

*Specifics*

LAU

fa.itp

O

lauroic acid

C11H23COOH

-



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


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

Deniz
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