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... <https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di...@nitk.edu.in&idSignature=22> On Fri, Aug 18, 2017 at 10:32 PM, Justin Lemkul <jalem...@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 > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- With Best Regards, DILIP.H.N Ph.D Student -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.