[gmx-users] grompp error in peptide-membrane simulations

afsaneh maleki maleki.afsaneh at gmail.com
Sat Sep 5 11:49:45 CEST 2009

I am working on memberane peptide simulation under lipid DOPC,i have
downloaded the lipid and dopc.itp from the same site,when i run grommp:
 ]grompp -f em.mdp  -c complex.gro  -o  em.tpr -p  complex.top
it gives me:
>Fetal error :
Atomtype LC3 not found! (this is atomtype of the lipide)
This is my  complex.top file
#include  "protein.itp"
#include "dopc.itp"
#include "lipid.itp"
#include "tip3p.itp"
#include "ions.itp"
protein on sur+relaxed dopc
;name    number
Protein  1
DOPC   128
SOL      4086
SOD      6
CLA       8
this atomtype (LC3) is in the dopc.itp and  lipid.itp files but don't find
in ffG43a2.rtp and .atp.
i'm sure structure file is n't different in terms of the number of atoms ,
atomnames and the order of them with .itp files.

any help will be hightly appreciated.

Afsaneh Maleki
PhD student of physical chemistry
Department of chemistry, Isfahan Univ. of Tech.
Isfahan 84156-83111, Iran
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090905/5342847c/attachment.html>

More information about the gromacs.org_gmx-users mailing list