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.
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$
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