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

[Mohsen Ramezanpour]

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

Best Regards


On Thu, Nov 28, 2013 at 6:13 PM, Justin Lemkul <jalemkul at 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.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
>
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