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

[Justin A. Lemkul]

afsaneh maleki wrote:
Hi,
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"
[system]
;name
protein on sur+relaxed dopc
[molecules]
;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.


Your topology file is set up incorrectly.  Might I suggest the tutorial I wrote 
for membrane protein simulations:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html

There is also helpful information on the wiki site (http://oldwiki.gromacs.org) 
about running membrane simulations and doing analysis.

-Justin

--
Afsaneh Maleki
PhD student of physical chemistry
Department of chemistry, Isfahan Univ. of Tech.
Isfahan 84156-83111, Iran


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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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