[gmx-users] Solvent error?

[Mark Abraham]

On Thu, Aug 14, 2014 at 9:55 AM, Nikolaos Michelarakis <nm884 at york.ac.uk>
wrote:

> Hello again,
>
> I am trying to include a ligand in my structure, which consists of 42
> atoms, using an .itp file, in the AMBER forcefield. The itp was generated
> by antechamber and is the ligand_backup.itp. Everything works fine until I
> try to solvate it. It seems that the gro file produced by the solvation
> includes 42 less atoms, therefore i get the following error when i try to
> run the energy minimization.
>
> Program gmx, VERSION 5.0
> Source code file:
>
> /home/jslatter/programs/gromacs/gromacs-5.0/src/gromacs/gmxpreprocess/grompp.c,
> line: 603
>
> Fatal error:
> number of coordinates in coordinate file (solv.gro, 57310)
>              does not match topology (fws.top, 57352)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> Are the 42 atoms of the ligand not included in the solv.gro file?
>

Presumably they were also missing from the input coordinate file.

Mark


>
> As usual, all the files that i have used are in the link:
>
>
> https://drive.google.com/folderview?id=0Bxa-J2wEpEeqOWFsOUUyNDVPYWc&usp=sharing
>
>
> Cheers,
>
> Nicholas
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