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.