[gmx-users] Fwd: Residue 1 mapping problem?
morpheus
morpheus.sommer2008 at gmail.com
Tue Aug 22 11:28:14 CEST 2017
Thanks!
Is this also just a note or is there a problem?
"
WARNING 1 [file md_vsIonDod.mdp]:
The sum of the two largest charge group radii (18.373196) is larger than
rlist (1.400000)
"
I found this on the gromacs webpage:
"A similar error ("The sum of the two largest charge group radii (X) is
larger than rlist") can arise under two circumstances:
1. The charge groups are inappropriately large or rlist is set too low.
2. Molecules are broken across periodic boundaries, which is not a
problem in a periodic system. In this case, the sum of the two largest
charge groups will correspond to a value of twice the box vector along
which the molecule is broken."
If I visualise my protein with VMD nothing seems to be broken across the
box boundary ...
Thanks!
M
---------- Forwarded message ----------
On 8/21/17 6:20 AM, morpheus wrote:
>* Hi,
*>>* I would like to simulate chain D and E of pdb-id 1oga but pdb2gmx complains
*>* about the first (?) residues of the 2 chains:
*>>* "WARNING: WARNING: Residue 1 named GLN 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."
*
This is an overly verbose message, which should not actually be a
"warning." Because you're requesting normal terminal patching (e.g.
NH3+), the H of residue 1 is deleted and will be replaced with H[123].
So this is really just telling you that's going on. It really shouldn't
be displayed, because it's confusing. But you receive no errors and you
can see that the topology was successfully generated.
-Justin
---------- Forwarded message ----------
From: morpheus <morpheus.sommer2008 at gmail.com>
Date: 2017-08-21 12:20 GMT+02:00
Subject: Residue 1 mapping problem?
To: gromacs.org_gmx-users at maillist.sys.kth.se
Hi,
I would like to simulate chain D and E of pdb-id 1oga but pdb2gmx complains
about the first (?) residues of the 2 chains:
"WARNING: WARNING: Residue 1 named GLN 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."
I assume it means this GLN (as it is the first residue of the file):
ATOM 3164 N GLN D 3 22.890 -35.428 -11.393 1.00
22.91 N
ATOM 3165 CA GLN D 3 21.681 -35.958 -10.698 1.00
21.34 C
ATOM 3166 C GLN D 3 20.599 -36.345 -11.695 1.00
20.99 C
ATOM 3167 O GLN D 3 20.336 -35.616 -12.646 1.00
22.83 O
ATOM 3168 CB GLN D 3 21.091 -34.889 -9.797 1.00
20.05 C
ATOM 3169 CG GLN D 3 21.926 -34.493 -8.608 1.00
20.82 C
ATOM 3170 CD GLN D 3 21.388 -33.220 -8.008 1.00
19.14 C
ATOM 3171 OE1 GLN D 3 21.602 -32.139 -8.553 1.00
21.07 O
ATOM 3172 NE2 GLN D 3 20.653 -33.341 -6.916 1.00
21.18 N
ATOM 3173 N LEU D 4 19.949 -37.480 -11.445 1.00
21.46 N
ATOM 3174 CA LEU D 4 18.889 -37.992 -12.300 1.00
22.61 C
ATOM 3175 C LEU D 4 17.679 -38.428 -11.487 1.00
20.04 C
ATOM 3176 O LEU D 4 17.814 -38.838 -10.337 1.00
21.78 O
ATOM 3177 CB LEU D 4 19.386 -39.229 -13.059 1.00
22.96 C
ATOM 3178 CG LEU D 4 20.637 -39.103 -13.912 1.00
26.17 C
ATOM 3179 CD1 LEU D 4 21.062 -40.497 -14.412 1.00
29.25 C
ATOM 3180 CD2 LEU D 4 20.341 -38.189 -15.071 1.00
27.56 C
Any ideas? My commands and gromacs output below.
Thanks!
[b at localhost newTry]$ gmx pdb2gmx -f JM22_fullMHC_fullTCR.pdb -o
JM22_fullMHC_fullTCR.gro -p JM22_fullMHC_fullTCR.top -i
JM22_fullMHC_fullTCR.posre.itp -ignh -vsite hydrogens
:-) GROMACS - gmx pdb2gmx, 2016.2 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par
Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios
Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund
Teemu Murtola Szilard Pall Sander Pronk Roland Schulz
Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx pdb2gmx, version 2016.2
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/b/data/projects/anton_mutationsMHC/complexes_
withConstTcrRegions/JM22_onlyTCR/newTry
Command line:
gmx pdb2gmx -f JM22_fullMHC_fullTCR.pdb -o JM22_fullMHC_fullTCR.gro -p
JM22_fullMHC_fullTCR.top -i JM22_fullMHC_fullTCR.posre.itp -ignh -vsite
hydrogens
Select the Force Field:
>From '/usr/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/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/share/gromacs/top/gromos53a6.ff/aminoacids.r2b
Reading JM22_fullMHC_fullTCR.pdb...
Read 3462 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 2 chains and 0 blocks of water and 439 residues with 3462 atoms
chain #res #atoms
1 'D' 199 1530
2 'E' 240 1932
All occupancies are one
Opening force field file /usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp
Atomtype 57
Reading residue database... (gromos53a6)
Opening force field file /usr/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/share/gromacs/top/gromos53a6.ff/aminoacids.hdb
Opening force field file /usr/share/gromacs/top/
gromos53a6.ff/aminoacids.n.tdb
Opening force field file /usr/share/gromacs/top/
gromos53a6.ff/aminoacids.c.tdb
Processing chain 1 'D' (1530 atoms, 199 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 298 donors and 310 acceptors were found.
There are 503 hydrogen bonds
Will use HISE for residue 76
Identified residue GLN3 as a starting terminus.
Identified residue SER201 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
CYS24 HIS76 CYS90 CYS134 MET163 MET166
SG177 NE2585 SG683 SG1003 SD1233 SD1258
HIS76 NE2585 1.658
CYS90 SG683 0.206 1.698
CYS134 SG1003 4.473 4.152 4.315
MET163 SD1233 3.926 3.135 3.791 2.051
MET166 SD1258 4.251 3.327 4.126 2.367 0.458
CYS184 SG1397 4.615 4.232 4.459 0.203 2.020 2.305
Linking CYS-24 SG-177 and CYS-90 SG-683...
Linking CYS-134 SG-1003 and CYS-184 SG-1397...
Start terminus GLN-3: NH3+
End terminus SER-201: COO-
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 199 residues with 1973 atoms
Chain time...
Making bonds...
Number of bonds was 2010, now 2005
Marked 442 virtual sites
Added 28 dummy masses
Added 85 new constraints
Generating angles, dihedrals and pairs...
WARNING: WARNING: Residue 1 named GLN 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 199 named SER 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: 3265 pairs
Before cleaning: 3814 dihedrals
Making cmap torsions...
There are 1067 dihedrals, 976 impropers, 2926 angles
3265 pairs, 2005 bonds and 413 virtual sites
Total mass 21753.295 a.m.u.
Total charge -4.000 e
Writing topology
Processing chain 2 'E' (1932 atoms, 240 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 385 donors and 375 acceptors were found.
There are 613 hydrogen bonds
Will use HISD for residue 31
Will use HISE for residue 137
Will use HISE for residue 154
Will use HISE for residue 167
Will use HISE for residue 207
Identified residue GLY5 as a starting terminus.
Identified residue ASP244 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
CYS25 HIS31 MET34 CYS93 HIS137 CYS145 HIS154
SG165 NE2217 SD237 SG724 NE21067 SG1125 NE21197
HIS31 NE2217 1.161
MET34 SD237 0.420 0.902
CYS93 SG724 0.202 1.161 0.334
HIS137 NE21067 5.135 5.406 5.315 5.112
CYS145 SG1125 3.301 3.963 3.619 3.334 2.514
HIS154 NE21197 1.827 2.820 2.150 1.822 4.006 1.887
HIS167 NE21309 2.618 2.926 2.885 2.688 3.033 1.490 2.132
HIS207 NE21629 3.945 4.507 4.294 4.031 2.925 1.241 2.823
CYS210 SG1657 3.201 3.842 3.524 3.244 2.597 0.203 1.871
HIS167 HIS207
NE21309 NE21629
HIS207 NE21629 1.710
CYS210 SG1657 1.313 1.139
Linking CYS-25 SG-165 and CYS-93 SG-724...
Linking CYS-145 SG-1125 and CYS-210 SG-1657...
Start terminus GLY-5: GLY-NH3+
End terminus ASP-244: COO-
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 240 residues with 2520 atoms
Chain time...
Making bonds...
Number of bonds was 2580, now 2575
Marked 587 virtual sites
Added 24 dummy masses
Added 87 new constraints
Generating angles, dihedrals and pairs...
WARNING: WARNING: Residue 1 named GLY 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 240 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: 4043 pairs
Before cleaning: 4985 dihedrals
Making cmap torsions...
There are 1329 dihedrals, 1338 impropers, 3775 angles
4043 pairs, 2575 bonds and 548 virtual sites
Total mass 27330.366 a.m.u.
Total charge -4.000 e
Writing topology
Including chain 1 in system: 2001 atoms 199 residues
Including chain 2 in system: 2544 atoms 240 residues
Now there are 4545 atoms and 439 residues
Total mass in system 49083.661 a.m.u.
Total charge in system -8.000 e
Writing coordinate file...
--------- PLEASE NOTE ------------
You have successfully generated a topology from: JM22_fullMHC_fullTCR.pdb.
The Gromos53a6 force field and the spc water model are used.
--------- ETON ESAELP ------------
GROMACS reminds you: "You Could Make More Money As a Butcher" (F. Zappa)
[b at localhost newTry]$
More information about the gromacs.org_gmx-users
mailing list