[gmx-users] phosphotyrosine peptide
Dear GMX users I performed a simulation on the complex composed of a protein and a peptide which has 2 residues phosphotyrosines using charmm36 force field in GROMACS. After that I used g_mmpbsa to calculate the binding energy and energy contribution per residue , but the binding energy was calculated + 426 kj/mol. I sent an email to gmmbsa mailing list and informed them , but they replied :" we have not tested the g_mmpbsa with charmm36 so we can't say about the validity. Other members of g_mmpbsa tool, also previously reported about the positive binding energy when using charmm36 force field." in fact they couldnt help me. as they noticed , it is because of using charmm36 ff. Is there anyone can help me which force field I should use in gromacs till I wont have any problem when I am going to use g-mmpbsa ? best regardsFarial -- 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.
[gmx-users] phosphotyrosine
Dear gmx users I used CHARMM36 ff to generate topology for my complex which has 2 phosphotyrosines. when I issed gmx pdb2gmx command , I faced to this error: Fatal error: Residue 1 named PRO of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in an interaction of type improper in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. I couldnt understand what it meant . my protein residue 1 is Gly and peptide residue 1 is Thr. there is no residue Pro in position 1 in both molecules. In addition, I checked merged.rtp file of CHARMM36 ff to compare pro residue in it with the input file , but everything sound be ok. I dont know , what should I do. I would really appreciate it if anybody helps me best Farial -- 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.
