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

[Mohsen Ramezanpour]

Thank you for your reply.
In this case it is easier to use -p option instead of manual modification
but both of them are possible. Of course In some cases we need to modify
.top files manually (protein-drug complex system).

Thanks again for information




On Thu, Nov 28, 2013 at 6:53 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
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