thanks for reply
On Fri, Sep 14, 2018 at 5:09 PM Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/14/18 6:48 AM, AKANXA TIWARI wrote: > > i am getting a warning after converting pdb2gmx and then applying force > > field what i will do. please help me.i get this on screen. > > WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was > > mapped > > to an entry in the topology database, but the atom H used in > > an interaction of type angle in that entry is not found in the > > input file. Perhaps your atom and/or residue naming needs to be > > fixed. > > > > > > > > WARNING: WARNING: Residue 374 named PHE of a molecule in the input file > was > > mapped > > to an entry in the topology database, but the atom O used in > > an interaction of type angle in that entry is not found in the > > input file. Perhaps your atom and/or residue naming needs to be > > fixed. > > > > pdb2gmx is just being a bit too noisy here. Termini are being patched, > which means some atoms get deleted, replaced, or added. Here, an > existing atom is being deleted and replaced with another at both the N- > and C-termini. There is no problem, as you see the message below about > successful completion. > > -Justin > > > Before cleaning: 6050 pairs > > Before cleaning: 7868 dihedrals > > Making cmap torsions... > > There are 2709 dihedrals, 1833 impropers, 5404 angles > > 6050 pairs, 3705 bonds and 0 virtual sites > > Total mass 40604.576 a.m.u. > > Total charge 11.000 e > > Writing topology > > > > Back Off! I just backed up posre.itp to ./#posre.itp.1# > > > > Writing coordinate file... > > > > Back Off! I just backed up actin_asp_processed.gro to > > ./#actin_asp_processed.gro.1# > > --------- PLEASE NOTE ------------ > > You have successfully generated a topology from: actin_asp_clean.pdb. > > The Gromos54a7 force field and the spce water model are used. > > --------- ETON ESAELP ------------ > > > > GROMACS reminds you: "Miggida-Miggida-Miggida-Mac" (Kriss Kross) > > > > akanxa@akanxa-HP-Notebook:~/Documents/aasp$ > > -- > ================================================== > > 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.thelemkullab.com > > ================================================== > > -- > 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. > -- 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.