[gmx-users] total charge (qtot)
Justin Lemkul
jalemkul at vt.edu
Thu May 14 03:19:05 CEST 2015
On 5/13/15 9:17 PM, James Lord wrote:
> ops silly one though, I meant just need to select solvent when asked right?
>
Please consult some basic tutorials where these routine operations are covered.
-Justin
> On Thu, May 14, 2015 at 1:13 PM, James Lord <jjamesgreen110 at gmail.com
> <mailto:jjamesgreen110 at gmail.com>> wrote:
>
> Thanks Justin,
>
> So Just adding +7 Na to the whole system should be good to go to next
> step? or do I need to neutralize each chain separately? If yes how?
>
> Cheers
> James
>
> On Thu, May 14, 2015 at 1:05 AM, Justin Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> On 5/13/15 9:04 AM, James Lord 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"
>
>
> You have multiple chains, each with a net charge. The qtot value is, in
> fact, printed to the topology, just in each chain's .itp file.
>
> -Justin
>
>
>
> 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
>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu
> <mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
> <tel:%28410%29%20706-7441>
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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