[gmx-users] pdb2gmx - how to prevent it from removing atoms?
Fiona Reid
fiona at epcc.ed.ac.uk
Thu Sep 2 12:15:54 CEST 2004
Dear Gromacs Users,
When using pdb2gmx with the -ignh option I've noticed
that large number of the atoms disappear when compared
with the original input file.
I start with an input pdb file containing a protein
(dihydrofolate reductase (dhfr)) which contains 159
residues and a total of 2489 atoms. After running
pdb2gmx with -ignh and my output pdb file contains
just 1602 atoms.
E.g when I ran: pdb2gmx -f test_nowater.pdb
The output was:
###########
<snip>
Looking whether force field file ffG43a1.rtp exists
Opening library file
/hpcx/home/z001/z001/fiona/gromacs/gromacs_3.2.1_qhot/share/top/ffG43a1.rtp
Opening library file
/hpcx/home/z001/z001/fiona/gromacs/gromacs_3.2.1_qhot/share/top/aminoacids.dat
Reading test_nowater.pdb...
Read 2489 atoms
Opening library file
/hpcx/home/z001/z001/fiona/gromacs/gromacs_3.2.1_qhot/share/top/xlateat.dat
23 out of 23 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 159 residues with 2489 atoms
chain #res #atoms
1 ' ' 159 2489
WARNING: there were 2415 atoms with zero occupancy and 64 atoms with
occupancy unequal to one (out of 2489 atoms). Check your pdb
file.
Opening library file
/hpcx/home/z001/z001/fiona/gromacs/gromacs_3.2.1_qhot/share/top/ffG43a1.atp
Atomtype 50
Reading residue database... (ffG43a1)
Opening library file
/hpcx/home/z001/z001/fiona/gromacs/gromacs_3.2.1_qhot/share/top/ffG43a1.rtp
Residue 96
Sorting it all out...
Opening library file
/hpcx/home/z001/z001/fiona/gromacs/gromacs_3.2.1_qhot/share/top/ffG43a1.hdb
Opening library file
/hpcx/home/z001/z001/fiona/gromacs/gromacs_3.2.1_qhot/share/top/ffG43a1-n.tdb
Opening library file
/hpcx/home/z001/z001/fiona/gromacs/gromacs_3.2.1_qhot/share/top/ffG43a1-c.tdb
Back Off! I just backed up topol.top to ./#topol.top.1#
Processing chain 1 (2489 atoms, 159 residues)
Opening library file
/hpcx/home/z001/z001/fiona/gromacs/gromacs_3.2.1_qhot/share/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
Special Atom Distance matrix:
CYS85
SG1334
CYS152 SG2349 2.692
There are 235 donors and 240 acceptors
There are 324 hydrogen bonds
Fatal error: Atom HA in residue MET 1 not found in rtp entry with 9 atoms
while sorting atoms. Maybe different protonation state.
Remove this hydrogen or choose a different protonation state.
Option -ignh will ignore all hydrogens in the input.
###########
So I then tried pdb2gmx again using -ignh as suggested: pdb2gmx -f -ignh
test_nowater.pdb
###########
<snip>
Looking whether force field file ffG43a1.rtp exists
Opening library file
/hpcx/home/z001/z001/fiona/gromacs/gromacs_3.2.1_qhot/share/top/ffG43a1.rtp
Opening library file
/hpcx/home/z001/z001/fiona/gromacs/gromacs_3.2.1_qhot/share/top/aminoacids.dat
Reading test_nowater.pdb...
Read 1268 atoms
Opening library file
/hpcx/home/z001/z001/fiona/gromacs/gromacs_3.2.1_qhot/share/top/xlateat.dat
23 out of 23 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 159 residues with 1268 atoms
chain #res #atoms
1 ' ' 159 1268
WARNING: there were 1227 atoms with zero occupancy and 37 atoms with
occupancy unequal to one (out of 1268 atoms). Check your pdb
file.
Opening library file
/hpcx/home/z001/z001/fiona/gromacs/gromacs_3.2.1_qhot/share/top/ffG43a1.atp
Atomtype 50
Reading residue database... (ffG43a1)
Opening library file
/hpcx/home/z001/z001/fiona/gromacs/gromacs_3.2.1_qhot/share/top/ffG43a1.rtp
Residue 96
Sorting it all out...
Opening library file
/hpcx/home/z001/z001/fiona/gromacs/gromacs_3.2.1_qhot/share/top/ffG43a1.hdb
Opening library file
/hpcx/home/z001/z001/fiona/gromacs/gromacs_3.2.1_qhot/share/top/ffG43a1-n.tdb
Opening library file
/hpcx/home/z001/z001/fiona/gromacs/gromacs_3.2.1_qhot/share/top/ffG43a1-c.tdb
Back Off! I just backed up topol.top to ./#topol.top.2#
Processing chain 1 (1268 atoms, 159 residues)
Opening library file
/hpcx/home/z001/z001/fiona/gromacs/gromacs_3.2.1_qhot/share/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
Special Atom Distance matrix:
CYS85
SG658
CYS152 SG1198 2.692
There are 235 donors and 240 acceptors
There are 324 hydrogen bonds
Checking for duplicate atoms....
deleting duplicate atom O ARG 159 pdb nr 2489
Now there are 1267 atoms
N-terminus: NH3+
C-terminus: COO-
Now there are 159 residues with 1602 atoms
Making bonds...
Warning: Long Bond (432-434 = 4.53792 nm)
Warning: Long Bond (434-436 = 0.620787 nm)
Warning: Long Bond (436-444 = 0.811458 nm)
Warning: Long Bond (444-445 = 0.855804 nm)
Warning: Long Bond (444-446 = 4.26874 nm)
Warning: Long Bond (437-438 = 0.710563 nm)
Warning: Long Bond (438-439 = 0.362155 nm)
Warning: Long Bond (438-441 = 0.540152 nm)
Warning: Long Bond (439-442 = 0.702567 nm)
Warning: Long Bond (441-443 = 1.03103 nm)
Warning: Long Bond (442-443 = 0.943403 nm)
Warning: Long Bond (1108-1110 = 4.11203 nm)
Warning: Long Bond (1112-1120 = 0.595517 nm)
Warning: Long Bond (1120-1121 = 0.812652 nm)
Warning: Long Bond (1120-1122 = 3.43465 nm)
Warning: Long Bond (1113-1114 = 0.420582 nm)
Warning: Long Bond (1114-1115 = 0.412845 nm)
Warning: Long Bond (1114-1117 = 0.58955 nm)
Warning: Long Bond (1117-1119 = 0.419076 nm)
Warning: Long Bond (1195-1197 = 3.8193 nm)
Warning: Long Bond (1197-1199 = 0.71018 nm)
Warning: Long Bond (1199-1207 = 0.335476 nm)
Warning: Long Bond (1207-1208 = 0.641443 nm)
Warning: Long Bond (1207-1209 = 3.04772 nm)
Warning: Long Bond (1199-1200 = 0.63493 nm)
Warning: Long Bond (1200-1201 = 0.301703 nm)
Warning: Long Bond (1201-1202 = 0.682551 nm)
Warning: Long Bond (1201-1204 = 0.583263 nm)
Warning: Long Bond (1202-1205 = 0.451491 nm)
Warning: Long Bond (1204-1206 = 0.380317 nm)
Warning: Long Bond (1205-1206 = 0.408119 nm)
Warning: Long Bond (1392-1394 = 4.42603 nm)
Warning: Long Bond (1394-1396 = 0.500049 nm)
Warning: Long Bond (1404-1405 = 0.806747 nm)
Warning: Long Bond (1404-1406 = 5.16887 nm)
Warning: Long Bond (1396-1397 = 0.318762 nm)
Warning: Long Bond (1397-1398 = 0.56807 nm)
Warning: Long Bond (1398-1399 = 0.670946 nm)
Warning: Long Bond (1399-1402 = 0.67489 nm)
Warning: Long Bond (1401-1403 = 0.414344 nm)
Warning: Long Bond (1402-1403 = 0.586277 nm)
Warning: Long Bond (1465-1467 = 5.21114 nm)
Warning: Long Bond (1469-1477 = 0.600607 nm)
Warning: Long Bond (1477-1478 = 0.367479 nm)
Warning: Long Bond (1477-1479 = 4.35932 nm)
Warning: Long Bond (1469-1470 = 0.732503 nm)
Warning: Long Bond (1472-1475 = 0.500016 nm)
Warning: Long Bond (1474-1476 = 0.542793 nm)
Warning: Long Bond (1475-1476 = 0.338945 nm)
Opening library file
/hpcx/home/z001/z001/fiona/gromacs/gromacs_3.2.1_qhot/share/top/aminoacids.dat
Number of bonds was 1641, now 1636
Generating angles, dihedrals and pairs...
Before cleaning: 2615 pairs
Before cleaning: 3155 dihedrals
There are 854 dihedrals, 841 impropers, 2392 angles
2615 pairs, 1636 bonds and 0 dummies
Total mass 17989.346 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 conf.gro to ./#conf.gro.1#
--------- PLEASE NOTE ------------
You have succesfully generated a topology from: test_nowater.pdb.
The select force field and the spc water model are used.
Note that the default mechanism for selecting a force fields has
changed, starting from GROMACS version 3.2.0
--------- ETON ESAELP ------------
###########
I then created a new pdb file using editconf:
editconf -f conf.gro -o test_gromacsout.pdb
Comparing the two pdb files in vmd it is obvious that a
large number of atoms are missing from the output pdb
file.
Any suggestions/solutions greatly appreciated.
Many thanks,
Fiona Reid
P.S. For info, I am attempting to run the Joint Amber-Charmm
benchmark on Gromacs 3.2.1. It's possible that someone else
may have tried this already and found a solution?
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