[gmx-users] Residue 'DEF' not found in residue topology database
Emine Deniz Tekin
edeniztekin at gmail.com
Wed Feb 23 14:36:14 CET 2011
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:
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?
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,
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