[gmx-users] total charge (qtot)
James Lord
jjamesgreen110 at gmail.com
Thu May 14 03:13:16 CEST 2015
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> 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 | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
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