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 <jjamesgreen...@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 <jalem...@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 >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> http://mackerell.umaryland.edu/~jalemkul >> >> ================================================== >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. > > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
