On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote:
Hi GMX Users, please help me
I am trying to begin a simulation of a protein and ligand coplex by 

I am using AMBER99sb-ILDN force field and TIP4P water model. However,
I am facing a problem in the ion adding step.

when  I issue the grompp command to generate the necessary .tpr file
for simulation to be utilised by genion tool, I get the following
error :

Fatal error:
number of coordinates in coordinate file (solv.gro, 102546)
does not match topology (topol.top, 133916)

whe i use tip3p, i don't get error.

Thank you very much

Use share/gromacs/top/tip4p.gro when generating the simulation box, tip4p has an aditional interaction site


T.M.D. Graen
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department, 105 00
Am Fassberg 11
37077 Goettingen, Germany
Tel.:  ++49 551 201 2313
Fax:  ++49 551 201 2302
Email: tgr...@gwdg.de
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