[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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