[gmx-users] total charge (qtot)
James Lord
jjamesgreen110 at gmail.com
Wed May 13 15:06:18 CEST 2015
I can see that I have two chains but can I simply say the total charge is
-7 e?
Cheers
James
On Thu, May 14, 2015 at 1:04 AM, James Lord <jjamesgreen110 at gmail.com>
wrote:
> 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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