On September 23, 2010 at 3:02 PM Artur Panczakiewicz <[email protected]> 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
> -------------------------------------------------------
> 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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> 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
> --
> gmx-users mailing list [email protected]
> 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 [email protected].
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>
TJ Mustard
Email: [email protected]
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