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

[Mohsen Ramezanpour]

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?
Please let me know



On Thu, Nov 28, 2013 at 6:37 PM, Mohsen Ramezanpour <
ramezanpour.mohsen at 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 <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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