Maybe you should modify your .tpr file manually according to what you added
in the previous sections!




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
>
> --
> --
> 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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