[gmx-users] total charge (qtot)
James Lord
jjamesgreen110 at gmail.com
Thu May 14 03:17:48 CEST 2015
ops silly one though, I meant just need to select solvent when asked right?
On Thu, May 14, 2015 at 1:13 PM, James Lord <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> 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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