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 
gromacs4.6.3.

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

best
timo

--
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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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