[gmx-users] Solvent error?
mark.j.abraham at gmail.com
Thu Aug 14 20:09:59 CEST 2014
On Thu, Aug 14, 2014 at 9:55 AM, Nikolaos Michelarakis <nm884 at york.ac.uk>
> 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:
> 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.
> As usual, all the files that i have used are in the link:
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