[gmx-users] pdb2gmx picks up the wrong .tdb files?
András Ferenc WACHA
wacha.andras at ttk.hu
Thu Jan 16 14:13:43 CET 2020
Dear fellow Gromacs users,
I have developed an extended version of the CHARMM36m force field for
beta-amino acids (https://charmm-betaff.readthedocs.io,
https://gitlab.com/awacha/charmm-beta.ff). For beta-amino acids I found
pdb2gmx works well. However, if I try to use it for natural peptides and
proteins (e.g. 6LYZ from the PDB), the following command:
gmx pdb2gmx -f 6LYZ.pdb, -ff charmm-beta -ter -ignh
fails to recognize the correct termini database files. The output is the
following:
(-------------------------- START of gmx output
-----------------------------------)
GROMACS: gmx pdb2gmx, version 2020
Executable:
/opt/spack/opt/spack/linux-archrolling-skylake/gcc-9.2.0/gromacs-2020-ls53yrft6droj2ovhuzdwdufi4an4vir/bin/gmx
Data prefix:
/opt/spack/opt/spack/linux-archrolling-skylake/gcc-9.2.0/gromacs-2020-ls53yrft6droj2ovhuzdwdufi4an4vir
Working dir: /home/wachaandras/gromacs/forcefields
Command line:
gmx pdb2gmx -f 6lyz.pdb -ff charmm-beta -ter -ignh
Using the Charmm-beta force field in directory ./charmm-beta.ff
Opening force field file ./charmm-beta.ff/watermodels.dat
Select the Water Model:
1: TIP3P TIP 3-point, recommended, by default uses CHARMM TIP3 with
LJ on H
2: TIP4P TIP 4-point
3: TIP5P TIP 5-point
4: SPC simple point charge
5: SPC/E extended simple point charge
6: Methanol Equilibrated methanol
7: Octanol Equilibrated octanol
8: None
1
going to rename ./charmm-beta.ff/merged.r2b
Opening force field file ./charmm-beta.ff/merged.r2b
Reading 6lyz.pdb...
WARNING: all CONECT records are ignored
Read '', 1001 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 129 residues with 1001 atoms
chain #res #atoms
1 'A' 129 1001
All occupancies are one
Opening force field file ./charmm-beta.ff/atomtypes.atp
Opening force field file ./charmm-beta.ff/betaaminoacids.atp
Opening force field file ./charmm-beta.ff/cyclicbeta.atp
Reading residue database... (Charmm-beta)
Opening force field file ./charmm-beta.ff/betaaminoacids.rtp
Opening force field file ./charmm-beta.ff/cyclicbeta.rtp
Opening force field file ./charmm-beta.ff/extra.rtp
Warning: file does not end with a newline, last line:
;
Opening force field file ./charmm-beta.ff/merged.rtp
Opening force field file ./charmm-beta.ff/merged.hdb
Opening force field file ./charmm-beta.ff/betaaminoacids.n.tdb
Opening force field file ./charmm-beta.ff/cyclicbeta.n.tdb
Opening force field file ./charmm-beta.ff/merged.n.tdb
Opening force field file ./charmm-beta.ff/betaaminoacids.c.tdb
Opening force field file ./charmm-beta.ff/cyclicbeta.c.tdb
Opening force field file ./charmm-beta.ff/merged.c.tdb
Processing chain 1 'A' (1001 atoms, 129 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 213 donors and 184 acceptors were found.
There are 262 hydrogen bonds
Will use HISD for residue 15
Identified residue LYS1 as a starting terminus.
Identified residue LEU129 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
CYS6 MET12 HIS15 CYS30 CYS64 CYS76 CYS80
SG48 SD87 NE2118 SG238 SG513 SG601 SG630
MET12 SD87 1.205
HIS15 NE2118 1.804 0.998
CYS30 SG238 1.450 1.070 2.063
CYS64 SG513 2.873 1.779 1.755 2.236
CYS76 SG601 2.740 1.544 1.418 2.132 0.778
CYS80 SG630 3.006 1.943 1.892 2.387 0.200 0.958
CYS94 SG724 2.576 1.388 1.329 1.976 0.678 0.211 0.871
MET105 SD799 1.866 0.933 1.679 0.896 1.858 1.483 2.047
CYS115 SG889 1.625 1.099 2.068 0.204 2.108 2.005 2.260
CYS127 SG981 0.203 1.089 1.733 1.332 2.808 2.631 2.950
CYS94 MET105 CYS115
SG724 SD799 SG889
MET105 SD799 1.389
CYS115 SG889 1.855 0.790
CYS127 SG981 2.474 1.701 1.505
Linking CYS-6 SG-48 and CYS-127 SG-981...
Linking CYS-30 SG-238 and CYS-115 SG-889...
Linking CYS-64 SG-513 and CYS-80 SG-630...
Linking CYS-76 SG-601 and CYS-94 SG-724...
Select start terminus type for LYS-1
0: Beta3NH3+
1: Beta2NH3+
2: Beta23NH3+
3: B3_NH2
4: B2_NH2
5: B23_NH2
6: 5TER
7: None
(-------------------------- END of gmx output
-----------------------------------)
Information in the force field relevant to the beta-peptides is stored
in betaaminoacids.{arn,atp,c.tdb,n.tdb,rtp} files. I have kept the
original ones (merged.*) intact. From the output above it seems that
pdb2gmx recognizes and loads all the relevant files (both
betaaminoacids.* and merged.*), but only shows a selection of N-terminal
patches from the betaaminoacids.n.tdb file. More precisely, the 5TER
terminus is from merged.n.tdb, but the other ones before it get
overridden by entries from betaaminoacids.n.tdb. Is there some rule in
pdb2gmx which considers some endgroups equivalent and keeps only one? I
have encountered it neither in the main documentation (section 5.6.5:
pdb2gmx input files), nor in the help of gmx pdb2gmx.
Could anyone point me to how I should do this correctly?
Kind regards,
Andras
--
András Ferenc Wacha, PhD
research fellow, CREDO instrument responsible
Biological Nanochemistry Research Group (310)
Institute of Materials and Environmental Chemistry
Research Centre for Natural Sciences (RCNS)
Magyar tudósok körútja 2.
H-1117 Budapest, Hungary
Phone: +36-1-382-6427
Web: http://bionano.ttk.hu
CREDO SAXS instrument: http://credo.ttk.hu
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