[gmx-users] force field

[mohammad r]

Thank you very much Maryam and Justin.unfortunately I am new to gromacs and MD.I think that I can acetylate or ammoniate my peptide with -ter attachment to pdb2gmx command. I think it works.What is the different between NH2+ and NH3 for ammoniation (the gromacs ask to choose one of them)? also ask for acetylation a similar question.Thanks, M.


     On Sunday, August 9, 2015 11:06 PM, Maryam Kowsar <maryam.kowsar at gmail.com> wrote:
   

 I did a similar task. You should know the parameters and convert your files
format to gromacs format. A bit difficult but possible.


On Sun, Aug 9, 2015 at 9:35 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/9/15 12:59 PM, mohammad r wrote:
>
>> Thank you MaryamI want to use this force field in the first step of
>> generating the topology file (pdb2gmx command in the force field shown
>> after this command). Is it possible? and unfortunately I don't know how to
>> find the necessary files of this force field. I searched a lot but I didn't
>> succeed.
>>
>
> If the force field files haven't been created already (in this case, they
> haven't) you have to convert the force field files from AMBER format to
> GROMACS format.  That's a pretty big undertaking if you're not well versed
> in the formats.
>
> I have another question, is it possible to acetylate or ammoniate a
>> peptide with gromacs?
>>
>
> Anything is possible, provided you have parameters for such species.
>
> -Justin
>
> thank you, M.
>>
>>
>>      On Sunday, August 9, 2015 8:17 PM, Maryam Kowsar <
>> maryam.kowsar at gmail.com> wrote:
>>
>>
>>  let me modify my previous message: in the g_x2top command, not grompp
>> :-)
>> On Sun, Aug 9, 2015 at 8:14 PM, Maryam Kowsar <maryam.kowsar at gmail.com>
>> wrote:
>>
>> Hi Mohammad,
>> Yes that's possible. You should just have the necessary files of your
>> desired forcefield(.atp,.itp,...), and put them in a folder. in the grompp
>> command just add -ff folder name. that's all! It will use your forcefield
>> instead of the present forcefields in gromacs.
>> Regards,-Maryam
>> On Sun, Aug 9, 2015 at 5:57 PM, mohammad r <mohammad.r0325 at yahoo.com>
>> wrote:
>>
>> Hi;
>> I want to use ff14SB Amberprotein force field. But it isn't included in
>> the gromacs force fields list.Is it possible to use this force field? How
>> can I add it in?Thank you, Mohammad.
>> --
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>>
>>
>>
>>
>>
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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