On 11/28/13 10:13 AM, Mohsen Ramezanpour wrote:
Dear Justin
I meant modifying  .top  file after adding some ions and water molecules
which could be equivalent to -p option as you mentioned.
What do you think about this?

That would be one possible solution, but it is not yet clear what the OP has done or failed to do correctly. One does not need to make manual modifications if -p has properly been used with genbox and genion. The fact that the coordinate file specifies fewer atoms than the topology suggests that perhaps the wrong water coordinates were used (e.g. a 3-point model instead of a 4-point model), as would happen if one follows tutorials too literally and specifies genbox -cs spc216.gro instead of -cs tip4p.gro.

Many things could be wrong. The OP needs to provide more details so we can stop guessing and arrive at a solution.

-Justin

Please let me know



On Thu, Nov 28, 2013 at 6:37 PM, Mohsen Ramezanpour <
ramezanpour.moh...@gmail.com> wrote:

Oh, I am sorry, I made a big mistake! :)

Best Regards


On Thu, Nov 28, 2013 at 6:13 PM, Justin Lemkul <jalem...@vt.edu> wrote:



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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Justin A. Lemkul, Ph.D.
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School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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