[gmx-users] Getting started - Peptide

[Justin A. Lemkul]

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 
there...

http://www.gromacs.org/Documentation/Errors#Fatal_error.3a_No_such_moleculetype_XXX

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.

-Justin

> Regards,
> Artur

-- 
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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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