[gmx-users] total charge (qtot)
James Lord
jjamesgreen110 at gmail.com
Wed May 13 15:04:08 CEST 2015
Dear gmx users,
I am trying to repeat Justin's Lysozyme tutorial for 1HFX.pdb,
https://drive.google.com/file/d/0B0YMTXH1gmQsUjVSd01ERXVpLTA/view?usp=sharing
I would like to know the total charge of my system but I have two statement
for that,after running
pdb2gmx -f 1HFX.pdb -o 1HFX_processed.gro -water spce
one is saying -9e and 2e? I am a bit confuse can anyone tell me why it is
like this? I also checked the topol.top and there is no "qtot"
pdb2gmx -f 1HFX.pdb -o 1HFX_processed.gro -water spce
:-) G R O M A C S (-:
Good ROcking Metal Altar for Chronical Sinners
:-) VERSION 4.6.3 (-:
Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2012,2013, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program 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.
:-) pdb2gmx (-:
Option Filename Type Description
------------------------------------------------------------
-f 1HFX.pdb Input Structure file: gro g96 pdb tpr etc.
-o 1HFX_processed.gro Output Structure file: gro g96 pdb etc.
-p topol.top Output Topology file
-i posre.itp Output Include file for topology
-n clean.ndx Output, Opt. Index file
-q clean.pdb Output, Opt. Structure file: gro g96 pdb etc.
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-chainsep enum id_or_ter Condition in PDB files when a new chain
should
be started (adding termini): id_or_ter,
id_and_ter, ter, id or interactive
-merge enum no Merge multiple chains into a single
[moleculetype]: no, all or interactive
-ff string select Force field, interactive by default. Use -h for
information.
-water enum spce Water model to use: select, none, spc, spce,
tip3p, tip4p or tip5p
-[no]inter bool no Set the next 8 options to interactive
-[no]ss bool no Interactive SS bridge selection
-[no]ter bool no Interactive termini selection, instead of
charged
(default)
-[no]lys bool no Interactive lysine selection, instead of charged
-[no]arg bool no Interactive arginine selection, instead of
charged
-[no]asp bool no Interactive aspartic acid selection, instead of
charged
-[no]glu bool no Interactive glutamic acid selection, instead of
charged
-[no]gln bool no Interactive glutamine selection, instead of
neutral
-[no]his bool no Interactive histidine selection, instead of
checking H-bonds
-angle real 135 Minimum hydrogen-donor-acceptor angle for a
H-bond (degrees)
-dist real 0.3 Maximum donor-acceptor distance for a H-bond
(nm)
-[no]una bool no Select aromatic rings with united CH atoms on
phenylalanine, tryptophane and tyrosine
-[no]ignh bool no Ignore hydrogen atoms that are in the coordinate
file
-[no]missing bool no Continue when atoms are missing, dangerous
-[no]v bool no Be slightly more verbose in messages
-posrefc real 1000 Force constant for position restraints
-vsite enum none Convert atoms to virtual sites: none, hydrogens
or aromatics
-[no]heavyh bool no Make hydrogen atoms heavy
-[no]deuterate bool no Change the mass of hydrogens to 2 amu
-[no]chargegrp bool yes Use charge groups in the .rtp file
-[no]cmap bool yes Use cmap torsions (if enabled in the .rtp file)
-[no]renum bool no Renumber the residues consecutively in the
output
-[no]rtpres bool no Use .rtp entry names as residue names
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 (with CMAP) - version 2.0
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)
16: [DEPRECATED] Encad all-atom force field, using full solvent charges
17: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum
charges
18: [DEPRECATED] Gromacs force field (see manual)
19: [DEPRECATED] Gromacs force field with hydrogens for NMR
15
Using the Oplsaa force field in directory oplsaa.ff
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.r2b
Reading 1HFX.pdb...
WARNING: all CONECT records are ignored
Read 'ALPHA-LACTALBUMIN', 1069 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
WARNING: Chain identifier 'A' is used in two non-sequential blocks.
They will be treated as separate chains unless you reorder your file.
There are 2 chains and 1 blocks of water and 197 residues with 1069 atoms
chain #res #atoms
1 'A' 123 995
2 'A' 1 1
3 ' ' 73 73 (only water)
All occupancies are one
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtypes.atp
Atomtype 1
Reading residue database... (oplsaa)
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.rtp
Residue 54
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb
Back Off! I just backed up topol.top to ./#topol.top.2#
Processing chain 1 'A' (995 atoms, 123 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 180 donors and 196 acceptors were found.
There are 262 hydrogen bonds
Will use HISE for residue 10
Will use HISD for residue 32
Will use HISE for residue 47
Will use HISE for residue 107
Identified residue LYS1 as a starting terminus.
Identified residue GLN123 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
CYS6 HIS10 CYS28 HIS32 HIS47 CYS61 CYS73
SG48 NE277 SG225 NE2262 NE2377 SG497 SG587
HIS10 NE277 0.715
CYS28 SG225 1.522 1.948
HIS32 NE2262 1.791 2.287 0.484
HIS47 NE2377 3.051 3.232 2.060 1.880
CYS61 SG497 2.817 2.797 2.313 2.287 1.017
CYS73 SG587 2.748 2.608 2.233 2.350 1.390 0.757
CYS77 SG615 2.932 2.917 2.465 2.415 1.078 0.203 0.934
MET90 SD718 2.683 2.405 2.447 2.639 1.913 1.131 0.544
CYS91 SG725 2.575 2.458 2.088 2.198 1.330 0.672 0.201
HIS107 NE2860 3.163 3.372 1.773 1.726 1.369 2.067 1.912
CYS111 SG890 1.677 2.062 0.202 0.475 1.889 2.183 2.098
CYS120 SG971 0.203 0.608 1.553 1.867 3.125 2.877 2.754
CYS77 MET90 CYS91 HIS107 CYS111
SG615 SD718 SG725 NE2860 SG890
MET90 SD718 1.271
CYS91 SG725 0.860 0.592
HIS107 NE2860 2.219 2.366 1.903
CYS111 SG890 2.339 2.344 1.960 1.576
CYS120 SG971 3.001 2.665 2.589 3.175 1.707
Linking CYS-6 SG-48 and CYS-120 SG-971...
Linking CYS-28 SG-225 and CYS-111 SG-890...
Linking CYS-61 SG-497 and CYS-77 SG-615...
Linking CYS-73 SG-587 and CYS-91 SG-725...
Start terminus LYS-1: NH3+
End terminus GLN-123: COO-
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 123 residues with 1955 atoms
Chain time...
Back Off! I just backed up topol_Protein_chain_A.itp to
./#topol_Protein_chain_A.itp.2#
Making bonds...
Number of bonds was 1978, now 1978
Generating angles, dihedrals and pairs...
Before cleaning: 5220 pairs
Before cleaning: 5265 dihedrals
Keeping all generated dihedrals
Making cmap torsions...There are 5265 dihedrals, 380 impropers, 3584 angles
5187 pairs, 1978 bonds and 0 virtual sites
Total mass 14206.088 a.m.u.
Total charge -9.000 e
Writing topology
Back Off! I just backed up posre_Protein_chain_A.itp to
./#posre_Protein_chain_A.itp.2#
Processing chain 2 'A' (1 atoms, 1 residues)
Warning: Starting residue CA124 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 1 residues with 1 atoms
Chain time...
Back Off! I just backed up topol_Ion_chain_A2.itp to
./#topol_Ion_chain_A2.itp.2#
Making bonds...
No bonds
Generating angles, dihedrals and pairs...
Making cmap torsions...There are 0 dihedrals, 0 impropers, 0 angles
0 pairs, 0 bonds and 0 virtual sites
Total mass 40.080 a.m.u.
Total charge 2.000 e
Writing topology
Back Off! I just backed up posre_Ion_chain_A2.itp to
./#posre_Ion_chain_A2.itp.2#
Processing chain 3 (73 atoms, 73 residues)
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 73 residues with 219 atoms
Making bonds...
Number of bonds was 146, now 146
Generating angles, dihedrals and pairs...
Making cmap torsions...There are 0 dihedrals, 0 impropers, 73 angles
0 pairs, 146 bonds and 0 virtual sites
Total mass 1315.124 a.m.u.
Total charge 0.000 e
Including chain 1 in system: 1955 atoms 123 residues
Including chain 2 in system: 1 atoms 1 residues
Including chain 3 in system: 219 atoms 73 residues
Now there are 2175 atoms and 197 residues
Total mass in system 15561.292 a.m.u.
Total charge in system -7.000 e
Writing coordinate file...
Back Off! I just backed up 1HFX_processed.gro to ./#1HFX_processed.gro.2#
--------- PLEASE NOTE ------------
You have successfully generated a topology from: 1HFX.pdb.
The Oplsaa force field and the spce water model are used.
--------- ETON ESAELP ------------
Cheers
James
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