[gmx-users] Getting started - Peptide

Justin A. Lemkul jalemkul at vt.edu
Thu Sep 23 16:05:59 CEST 2010

Artur Panczakiewicz wrote:
> Dear Gromacs Users,
> I'm a freshman and would like to lear how to use GROMACS in my
> research starting from tutorial. I've just installed the newest
> version and try to repeat all of the steps from the chapter that
> describes the preparation of Ribonuclease A to MD simulation. In my
> case it is not possible, unfortunatelly. The grompp program crashes
> such a way:
> -------------------------------------------------------
> Program grompp, VERSION 4.5.1
> Source code file: toppush.c, line: 1987
> Fatal error:
> No such moleculetype SOL
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> I tried to install GROMACS on other machine with different Linux
> distribution but the error in grompp was the same.
> What is important, I installed version 4.0.7 and it works well! I
> don't have any idea what is going on.
> Does anyone have a similar problem?

Did you follow the link provided by grompp?  There is some helpful information 


Was there water in the input structure?  There have been some changes to pdb2gmx 
since the 4.0.x series, perhaps related to the way water is named/renamed. 
Check what is in your coordinate file (before pdb2gmx and after), what is in 
your topology, and whether any of this is wrong or unexpected.


> Regards,
> Artur


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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