[gmx-users] simulation of membrane protein

[Justin A. Lemkul]

shikha agarwal wrote:
> Hi,
> 
> I have a problem with Gromacs. I want to do MD simulations with my 
> membrane proteïn in a POPE-membrane. Therefore I followed Justin 
> Lemkul's tutorial on membrane proteïn simulation.  I want to add ions. 
> But when I use grompp to get a .tpr
> 
> file for genion, Gromacs fives the following error:
> 
> /Program grompp, VERSION 4.0.7
> 
> Source code file: ../../gromacs-4.0.7/src/kernel/grompp.c, line: 320/
> /Fatal error:
> No molecules were defined in the system
> /
> 
>  help me.
> 

There are two likely reasons this error arises:

1. You have badly mangled your coordinate file, such that grompp cannot 
determine the proper number of atoms in it.
2. You haven't updated your [molecules] directive in the .top.

I would suggest you take another look through the tutorial, as topology 
organization and coordinate file construction are both discussed in depth.

-Justin

> shikha agarwal
> IIIT-A
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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