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... 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....
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 Thu, Aug 17, 2017 at 5:41 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/17/17 12:01 AM, Dilip H N wrote: > >> Thank you Justin Sir for replying... >> Yes, the term "dipeptide" is ambiguous.... >> But is there any other smallest molecule with an amide linkage (two >> aminoacids linked through peptide bond) or any other small peptide >> molecule >> that can be found in CHARMM36 FF.. with the corresponding residue naming >> in charmm... >> > > As I said, no, there's not. You have the smallest possible polypeptide, > two amino acids linked in the normal way. So that means you have a > sequence of GLY GLY, and the tool to produce that topology is pdb2gmx. > > -Justin > > Thank you... >> >> >> >> <https://mailtrack.io/> Sent with Mailtrack >> <https://mailtrack.io/install?source=signature&lang=en&refer >> ral=cy16f01.di...@nitk.edu.in&idSignature=22> >> >> >> On Wed, Aug 16, 2017 at 9:26 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> On 8/16/17 11:41 AM, Dilip H N wrote: >>> >>> Hello, >>>> I want to simulate a small dipeptide with mixture of solvents in >>>> charmm36 >>>> forcefield, (the solvents are already in charmm36 forcefield), but i am >>>> unable to find any small dipeptide molecule in charmm36 FF, since i have >>>> solvent molecules in charmm36 FF, but not the dipeptide, which would >>>> also >>>> be easy in getting the topology file by gmx pdb2gmx command... >>>> So can anybody help me how to find the dipeptide molecules (eg., >>>> diglycine) >>>> in charmm36 FF...?? >>>> >>>> There is no such special residue. For diglycine, you have two GLY. It's >>> like any peptide sequence. The only dipeptide that CHARMM has is alanine >>> dipeptide, but it's not ALA-ALA, it's ALA capped with acetyl and N-methyl >>> groups, so there are two peptide bonds, but not two residues (hence why >>> the >>> term "dipeptide" is ambiguous). >>> >>> -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. >>> >>> >> >> > -- > ================================================== > > 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.