[gmx-users] Getting started - Peptide

[Artur Panczakiewicz]

Hi All,

Thank you very much for suggestions!
It turned out that there was a missing entry in the top file.
After adding the following:
#include "spc.itp"
grommp finished without any errors :-)

Cheers,
Artur

2010/9/23 TJ Mustard <mustardt at onid.orst.edu>:
> On September 23, 2010 at 3:02 PM Artur Panczakiewicz
> <apanczakiewicz at gmail.com> 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
>> -------------------------------------------------------
>
>
>
> This usually means you have "SOL" coupled to a temperature, and if you don't
> have SOL in your system/.top/.gro you will get this error. This coupling is
> in the .mdp file. If you are running the system in a vacuum you must remove
> the SOL from the mdp file. If you want some kind of SOL (SPC, TIP3P, etc),
> you must add this in by making a box with solvent in it. The tutorial will
> most likely have this in it.
>
>
>
>
>
>> > 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?
>>
>> Regards,
>> Artur
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>
>
>
> TJ Mustard
> Email: mustardt at onid.orst.edu
>
> --
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