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On September 23, 2010 at 3:02 PM Artur Panczakiewicz <apanczakiewicz@gmail.com> wrote:<br />
<br />
> Dear Gromacs Users,<br />
><br />
> I'm a freshman and would like to lear how to use GROMACS in my<br />
> research starting from tutorial. I've just installed the newest<br />
> version and try to repeat all of the steps from the chapter that<br />
> describes the preparation of Ribonuclease A to MD simulation. In my<br />
> case it is not possible, unfortunatelly. The grompp program crashes<br />
> such a way:<br />
><br />
> -------------------------------------------------------<br />
> Program grompp, VERSION 4.5.1<br />
> Source code file: toppush.c, line: 1987<br />
><br />
> Fatal error:<br />
> No such moleculetype SOL<br />
> For more information and tips for troubleshooting, please check the GROMACS<br />
> website at http://www.gromacs.org/Documentation/Errors<br />
> -------------------------------------------------------<br />
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<p style="margin: 0px;">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.</p>
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> > I tried to install GROMACS on other machine with different Linux<br />
> distribution but the error in grompp was the same.<br />
> What is important, I installed version 4.0.7 and it works well! I<br />
> don't have any idea what is going on.<br />
> Does anyone have a similar problem?<br />
><br />
> Regards,<br />
> Artur<br />
> --<br />
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><br />
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<p style="font-family: monospace; white-space: nowrap; margin: 5px 0px 5px 0px;">TJ Mustard<br />
Email: mustardt@onid.orst.edu</p>
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