[gmx-users] Regarding naming dipeptide in charmm36 Forcefield
Dilip H N
cy16f01.dilip at nitk.edu.in
Sun Aug 20 21:16:08 CEST 2017
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....
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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
>> (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 A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
> jalemkul at vt.edu | (540) 231-3129
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With Best Regards,
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