[gmx-users] force field

[mohammad r]

thank you all for answering my question 


     On Monday, August 10, 2015 2:29 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
   

 

On 8/9/15 5:51 PM, mohammad r wrote:
> 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.
>

Acetylation requires the presence of an acetyl cap, which GROMACS will not build 
for you.  When capping, use "None" as the terminus selection.  The difference 
between NH2 and NH3+ is the protonation state.  This is a fundamental principle 
in (bio)chemistry dealing with the pKa of the group and pH of the solution. 
Undergraduate textbooks cover what this means, which you should familiarize 
yourself with long before touching anything related to an MD simulation.

-Justin

>
> 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. -- Gromacs Users mailing list
>>>
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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
>>
>> ==================================================
>>
>> -- Gromacs Users mailing list
>>
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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

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