[gmx-users] Regarding naming dipeptide in charmm36 Forcefield

[Dilip H N]

Have you run pdb2gmx to process a simple protein or polypeptide? This is
done for you.  Each amino acid is defined.  If you supply a coordinate file
with a GLY-GLY peptide, pdb2gmx does everything you need.
No Sir,  are thr any tutorials on polypeptide pdb generation and getting
the topology (pdb2gmx process).., which would be highly beneficial....

Thank you...


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On Fri, Aug 18, 2017 at 10:32 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/18/17 1:13 AM, Dilip H N wrote:
>
>> Thank you sir.,
>> 1] If so thn, is there any other possible way such that i can get a
>> peptide
>> (two aminoacids linked) and thn simulate it in CHARMM FF.. ?? (or) in
>> alanine dipeptide case which is the residue name in the .rtp file..?? and
>> how can i remove the n-methyl and  acetyl groups in order to get only
>> alanine dipeptide...
>>
>
> This doesn't make any sense to me.  The capping groups are what make
> alanine dipeptide (ALAD) what it is, not removing them.
>
> If you need to *generate* coordinates, then that's another matter. Plenty
> of software can do that (see links on gromacs.org).
>
> 2] Or should i modify modify any aminoacid (eg., glycine into diglycine)
>> into a peptide to run the simulation, and if so thn how can i take care of
>> charges in the peptide (since thee will be removal of H2O molecule between
>> them and diglycine case there will be some net charge resulting )..
>> I am running out of ideas....So any suggestions are welcome....
>>
>
> Have you run pdb2gmx to process a simple protein or polypeptide? This is
> done for you.  Each amino acid is defined.  If you supply a coordinate file
> with a GLY-GLY peptide, pdb2gmx does everything you need.
>
> -Justin
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
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>
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>
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-- 
With Best Regards,

DILIP.H.N
Ph.D Student