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

[Justin Lemkul]

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.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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>>
>>

-- 
==================================================

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

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