[gmx-users] gromacs warning topology file naming residues
Upasana Ray
upasanaray117 at gmail.com
Thu May 5 13:58:36 CEST 2016
pdb2gmx -f receptor.pdb -o recep.gro -p recep.top -i recep.itp
GROMACS: gmx pdb2gmx, VERSION 5.0.7
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Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
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Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
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and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
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check out http://www.gromacs.org for more information.
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GROMACS: gmx pdb2gmx, VERSION 5.0.7
Executable: /usr/local/gromacs/bin/gmx
Library dir: /usr/local/gromacs/share/gromacs/top
Command line:
pdb2gmx -f receptor.pdb -o recep.gro -p recep.top -i recep.itp
Select the Force Field:
>From '/usr/local/gromacs/share/gromacs/top':
1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24,
1999-2012, 2003)
2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29,
461-469, 1996)
4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21,
1049-1074, 2000)
5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65,
712-725, 2006)
6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al.,
Proteins 78, 1950-58, 2010)
7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
9: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI:
10.1007/s00249-011-0700-9)
15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
13
Using the Gromos53a6 force field in directory gromos53a6.ff
Opening force field file
/usr/local/gromacs/share/gromacs/top/gromos53a6.ff/watermodels.dat
Select the Water Model:
1: SPC simple point charge, recommended
2: SPC/E extended simple point charge
3: None
1
Opening force field file
/usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b
Reading receptor.pdb...
Read 2712 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 318 residues with 2712 atoms
chain #res #atoms
1 ' ' 318 2712
All occupancies are one
Opening force field file
/usr/local/gromacs/share/gromacs/top/gromos53a6.ff/atomtypes.atp
Atomtype 57
Reading residue database... (gromos53a6)
Opening force field file
/usr/local/gromacs/share/gromacs/top/gromos53a6.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/gromos53a6.ff/aminoacids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb
Back Off! I just backed up recep.top to ./#recep.top.6#
Processing chain 1 (2712 atoms, 318 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 476 donors and 475 acceptors were found.
There are 712 hydrogen bonds
Will use HISE for residue 148
Will use HISE for residue 179
Identified residue MET1 as a starting terminus.
Identified residue ASP318 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET1 MET18 CYS36 CYS44 MET49 CYS60 CYS94
SD8 SD144 SG292 SG356 SD397 SG492 SG794
MET18 SD144 1.598
CYS36 SG292 6.667 5.296
CYS44 SG356 8.837 7.478 2.301
MET49 SD397 10.320 8.864 3.717 2.019
CYS60 SG492 13.450 11.986 6.872 4.783 3.248
CYS94 SG794 20.844 19.314 14.849 12.884 11.492 8.577
CYS99 SG841 22.213 20.670 16.284 14.366 12.923 10.043 1.579
HIS148 NE21277 23.143 21.630 17.270 15.289 13.987 11.063 2.579
HIS179 NE21548 24.321 22.789 18.768 16.961 15.616 12.926 4.556
MET181 SD1563 23.994 22.477 18.367 16.490 15.207 12.443 3.998
MET214 SD1855 21.702 20.197 16.275 14.484 13.302 10.765 3.263
MET235 SD2024 24.164 22.667 18.421 16.451 15.230 12.351 3.974
MET248 SD2135 24.492 23.027 19.098 17.218 16.146 13.471 5.495
CYS249 SG2143 24.861 23.398 19.596 17.768 16.707 14.109 6.178
MET287 SD2464 21.466 20.208 15.629 13.392 12.875 10.149 7.761
MET297 SD2547 21.781 20.638 15.983 13.755 13.447 10.951 10.338
CYS99 HIS148 HIS179 MET181 MET214 MET235 MET248
SG841 NE21277 NE21548 SD1563 SD1855 SD2024 SD2135
HIS148 NE21277 1.732
HIS179 NE21548 3.220 2.776
MET181 SD1563 2.836 1.878 1.129
MET214 SD1855 2.963 2.777 2.881 2.451
MET235 SD2024 3.082 1.461 2.444 1.367 3.057
MET248 SD2135 4.758 3.374 2.938 2.246 3.206 2.139
CYS249 SG2143 5.371 4.119 3.093 2.703 3.584 2.906 0.891
MET287 SD2464 8.760 8.018 10.596 9.499 9.043 8.375 9.193
MET297 SD2547 11.405 10.810 13.480 12.399 11.992 11.253 12.199
CYS249 MET287
SG2143 SD2464
MET287 SD2464 10.006
MET297 SD2547 13.024 3.061
Start terminus MET-1: NH3+
End terminus ASP-318: COO-
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 318 residues with 3025 atoms
Making bonds...
Number of bonds was 3063, now 3058
Generating angles, dihedrals and pairs...
WARNING: WARNING: Residue 1 named MET 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 318 named ASP 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: 5315 pairs
Before cleaning: 5784 dihedrals
Making cmap torsions...
There are 1702 dihedrals, 1403 impropers, 4425 angles
5315 pairs, 3058 bonds and 0 virtual sites
Total mass 34482.681 a.m.u.
Total charge -8.000 e
Writing topology
Back Off! I just backed up recep.itp to ./#recep.itp.2#
Writing coordinate file...
Back Off! I just backed up recep.gro to ./#recep.gro.2#
--------- PLEASE NOTE ------------
You have successfully generated a topology from: receptor.pdb.
The Gromos53a6 force field and the spc water model are used.
--------- ETON ESAELP ------------
gcq#139: "One Ripple At a Time" (Bianca's Smut Shack)
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