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