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

========================================
--
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Reply via email to