GROMACS version: 5.1.4
GROMACS modification: Yes/No
Dear all,
When we run gmx pdb2gmx -f a.pdb -o a.gro -p a.top command it shows warning of mapping what does it mean and how to resolve it ?
Read 318 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 42 residues with 318 atoms
chain #res #atoms
1 ‘A’ 42 318
All occupancies are one
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/atomtypes.atp
Atomtype 58
Reading residue database… (gromos54a7)
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H–H interactions
Using default: removing proper dihedrals found on the same bond as a proper dihedral
Residue 108
Sorting it all out…
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.hdb
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb
Processing chain 1 ‘A’ (318 atoms, 42 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 58 donors and 59 acceptors were found.
There are 84 hydrogen bonds
Will use HISE for residue 6
Will use HISE for residue 13
Will use HISE for residue 14
Identified residue ASP1 as a starting terminus.
Identified residue ALA42 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
HIS6 HIS13 HIS14
NE254 NE2110 NE2120
HIS13 NE2110 1.658
HIS14 NE2120 1.503 1.161
MET35 SD275 3.762 3.417 2.667
Start terminus ASP-1: NH3+
End terminus ALA-42: COO-
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.
Now there are 42 residues with 409 atoms
Making bonds…
Number of bonds was 420, now 415
Generating angles, dihedrals and pairs…
WARNING: WARNING: Residue 1 named ASP 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 42 named ALA 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: 646 pairs
Before cleaning: 873 dihedrals
Making cmap torsions…
There are 285 dihedrals, 219 impropers, 610 angles
646 pairs, 415 bonds and 0 virtual sites
Total mass 4511.089 a.m.u.
Total charge -3.000 e
Writing topology
Writing coordinate file…
Hi,
The warning reports an inconsistency between the name in pdb file and the name in the force field database for aminoacids
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.rtp
you can look at the force field database entry and adapt the atom name in your pdb file in line with database definition.
Best regards
Alessandra
thank you for your suggestion
In this case, the warnings are meaningless and I would argue this is an output bug on the part of pdb2gmx (one that has existed for several years now). The warnings pertain to your termini, which are being patched and therefore some atom names are changing. pdb2gmx is changing those names, then complaining that it can’t find the old name. That’s exactly what it should be doing, so the output doesn’t make sense.
In any case, the command completed without any error (in GROMACS, errors and warnings are different, and here only errors matter) so you do not need to take any action.