[gmx-users] AMBER99sb-ILDN force field and TIP4P water model

[Justin Lemkul]

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.eslami at 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 <tgraen at 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: tgraen at gwdg.de
>> --
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

==================================================