On 11/28/13 9:37 AM, Mohsen Ramezanpour wrote:
Maybe you should modify your .tpr file manually according to what you added
in the previous sections!


Manually modify a .tpr?  How would one do that?

The OP needs to provide the exact commands issued. The fatal error shown results from poor bookkeeping (i.e. not making use of the -p option of genbox and genion) or use of the wrong water coordinate file.

I would also suggest some basic tutorial material to become more familiar with simple Gromacs tasks.

-Justin




On Thu, Nov 28, 2013 at 5:53 PM, Mahboobeh Eslami <
mahboobeh.esl...@yahoo.com> wrote:

dear timo
Please send me further details. I'm not a professional.
Thanks and regards




On Thursday, November 28, 2013 4:28 PM, Timo Graen <tgr...@gwdg.de> wrote:

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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