[gmx-users] Solvent error?

[Nikolaos Michelarakis]

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?

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