Re: [gmx-users] Atomistic Simulation
On 12/5/13 4:39 AM, panzu wrote: Where do I take that file from? The standard force field files located in $GMXLIB. Consult the manual and/or any basic tutorial. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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.
Re: [gmx-users] Atomistic Simulation
Where do I take that file from? -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013092.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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.
Re: [gmx-users] Atomistic Simulation
On 12/4/13 9:50 AM, panzu wrote: The thing is when I tray to use the grompp comand: bash >> g_grompp -f grompp.mdp -c tolu.pdb -p topol.top Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5# NOTE 1 [file grompp.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy --- Program g_grompp, VERSION 4.5.7 Source code file: /builddir/build/BUILD/gromacs-4.5.7/src/kernel/topio.c, line: 656 Fatal error: Syntax error - File tolu.itp, line 58 Last line read: '[ moleculetype ]' Invalid order for directive moleculetype For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I do not why it crashes ... This is how my topol looks like #include "tolu.itp" You need to define a parent force field before you can define molecules. See Chapter 5 of the manual. -Justin [ system ] Toluene [ molecules ] _I0L 10 -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013065.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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.
Re: [gmx-users] Atomistic Simulation
The thing is when I tray to use the grompp comand: bash >> g_grompp -f grompp.mdp -c tolu.pdb -p topol.top Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5# NOTE 1 [file grompp.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy --- Program g_grompp, VERSION 4.5.7 Source code file: /builddir/build/BUILD/gromacs-4.5.7/src/kernel/topio.c, line: 656 Fatal error: Syntax error - File tolu.itp, line 58 Last line read: '[ moleculetype ]' Invalid order for directive moleculetype For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I do not why it crashes ... This is how my topol looks like #include "tolu.itp" [ system ] Toluene [ molecules ] _I0L 10 -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013065.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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.
Re: [gmx-users] Atomistic Simulation
You don't need to. Gromacs accepts pdb, gro and several other coordinate file formats. On 4 Dec 2013 14:30, panzu wrote: so How do I convert from .pdb to .gro? -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013059.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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. - Sunday Times Scottish University of the Year 2011-2013 Top in the UK for student experience Fourth university in the UK and top in Scotland (National Student Survey 2012) We invite research leaders and ambitious early career researchers to join us in leading and driving research in key inter-disciplinary themes. Please see www.hw.ac.uk/researchleaders for further information and how to apply. Heriot-Watt University is a Scottish charity registered under charity number SC000278. -- 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.
Re: [gmx-users] Atomistic Simulation
Hi there, you can use editconf -f file.pdb -o file.gro Cheers, Ricardo. --- Biological Chemistry and Physics Faculty of Pharmaceutical Sciences at Ribeirão Preto University of São Paulo - Brazil - Mensagem original - > De: "panzu" > Para: gmx-us...@gromacs.org > Enviadas: Quarta-feira, 4 de Dezembro de 2013 12:06:28 > Assunto: Re: [gmx-users] Atomistic Simulation > so How do I convert from .pdb to .gro the ? > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013058.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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.
Re: [gmx-users] Atomistic Simulation
On Dec 4, 2013, at 3:06 PM, panzu wrote > so How do I convert from .pdb to .gro the ? Use editconf. Carsten -- 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.
Re: [gmx-users] Atomistic Simulation
You don't need to. Later processing steps such as editconf, genbox and grompp can read .pdb files. > so How do I convert from .pdb to .gro the ? > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013058.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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.
Re: [gmx-users] Atomistic Simulation
On 12/4/13 9:06 AM, panzu wrote: so How do I convert from .pdb to .gro the ? You don't technically need one: http://www.gromacs.org/Documentation/File_Formats/Coordinate_File If you prefer to use .gro format, just convert with editconf. The job of pdb2gmx is to produce a topology; the output of a force field-compliant structure is a side effect. You already have a matching structure and a topology, so there's no need to run pdb2gmx. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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.
Re: [gmx-users] Atomistic Simulation
so How do I convert from .pdb to .gro? -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013059.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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.
Re: [gmx-users] Atomistic Simulation
so How do I convert from .pdb to .gro the ? -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013058.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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.
Re: [gmx-users] Atomistic Simulation
On 12/4/13 6:15 AM, panzu wrote: Hello users, After downloading the toluene.pdb file of a toluene molecule and its forcefield tolu.itp from "Automated Topology Builder" and saved in the root /usr/share/gromacs/top/gromos53a6.ff I use the next comand i order to convert the pdb format to .gro : *** bash >> g_pdb2gmx -f tolu.pdb -o tolu.gro -i tolu.itp Select the Force Field: From '/usr/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: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 15: [DEPRECATED] Encad all-atom force field, using full solvent charges 16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges 17: [DEPRECATED] Gromacs force field (see manual) 18: [DEPRECATED] Gromacs force field with hydrogens for NMR 13 Using the Gromos53a6 force field in directory gromos53a6.ff Opening force field file /usr/share/gromacs/top/gromos53a6.ff/watermodels.dat Select the Water Model: 1: SPCsimple point charge, recommended 2: SPC/E extended simple point charge 3: None 3 Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b Reading tolu.pdb... WARNING: all CONECT records are ignored Read 'ALL ATOM STRUCTURE FOR MOLECULE 0', 15 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 0 residues with 15 atoms chain #res #atoms 1 ' ' 1 15 All occupancies are one Opening force field file /usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp Atomtype 1 Reading residue database... (gromos53a6) Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper Residue 108 Sorting it all out... Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.7# Processing chain 1 (15 atoms, 1 residues) Warning: Starting residue _I0L0 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 --- Program g_pdb2gmx, VERSION 4.5.7 Source code file: /builddir/build/BUILD/gromacs-4.5.7/src/kernel/resall.c, line: 581 Fatal error: Residue '_I0L' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- "You Own the Sun" (Throwing Muses) * I checked the residue "_I0L" and is defined in the tolu.itp Why do I get this error? Am I missing something?? Why are you running pdb2gmx? ATB provides you with the topology that you need. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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.
Re: [gmx-users] Atomistic Simulation
Hello users, After downloading the toluene.pdb file of a toluene molecule and its forcefield tolu.itp from "Automated Topology Builder" and saved in the root /usr/share/gromacs/top/gromos53a6.ff I use the next comand i order to convert the pdb format to .gro : *** bash >> g_pdb2gmx -f tolu.pdb -o tolu.gro -i tolu.itp Select the Force Field: >From '/usr/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: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 15: [DEPRECATED] Encad all-atom force field, using full solvent charges 16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges 17: [DEPRECATED] Gromacs force field (see manual) 18: [DEPRECATED] Gromacs force field with hydrogens for NMR 13 Using the Gromos53a6 force field in directory gromos53a6.ff Opening force field file /usr/share/gromacs/top/gromos53a6.ff/watermodels.dat Select the Water Model: 1: SPCsimple point charge, recommended 2: SPC/E extended simple point charge 3: None 3 Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b Reading tolu.pdb... WARNING: all CONECT records are ignored Read 'ALL ATOM STRUCTURE FOR MOLECULE 0', 15 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 0 residues with 15 atoms chain #res #atoms 1 ' ' 1 15 All occupancies are one Opening force field file /usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp Atomtype 1 Reading residue database... (gromos53a6) Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper Residue 108 Sorting it all out... Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.7# Processing chain 1 (15 atoms, 1 residues) Warning: Starting residue _I0L0 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 --- Program g_pdb2gmx, VERSION 4.5.7 Source code file: /builddir/build/BUILD/gromacs-4.5.7/src/kernel/resall.c, line: 581 Fatal error: Residue '_I0L' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- "You Own the Sun" (Throwing Muses) * I checked the residue "_I0L" and is defined in the tolu.itp Why do I get this error? Am I missing something?? Thanks in advance!! Sergio -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013044.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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.
Re: [gmx-users] Atomistic Simulation
Thanks you all for the suggestions. I wil try then... -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013039.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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.
Re: [gmx-users] Atomistic Simulation
I've used the ATB, there kinda the replacment for the PRODGR, which is now commercial. They do have the same problems though, such as 99% correct output, and then manual changes for something (example: an NH2 on the side of a ring parameterized as an NH3, so acts as such...needs to be changed, but you may not notice it until short simulations are run, with all other atoms out of 30-40 correct...). Stephan Watkins Gesendet: Dienstag, 03. Dezember 2013 um 12:17 Uhr Von: "Hardy, Adam" An: "gmx-us...@gromacs.org" Betreff: Re: [gmx-users] Atomistic Simulation I've just started doing atomistic simulations over the last few weeks as well and can share what I've learned so far. I have been using 'automated topology builder'. It only uses the gromos 53a6 forcefield so eliminates the choice if you want to use it. ATB generates the pdb and itp files for you. There are a lot of molecules already on there or you can submit you're own using a _javascript_ molecule builder. There may well be other ways to do this but I haven't found them yet. On 3 Dec 2013 10:14, panzu wrote: Hello to everybody, I am new in atomistic simulations and a have some doubts about how to do it. I wanna simulate a mixture of Cyclohexane, Toluene and Dodecane. My questions are, ¿Where do I get the pdb files of these molecules from? and ¿How do I know which force field I should choose in pdb2gmx in order to make the itp file? Thanks in advance, Panzu -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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. - Sunday Times Scottish University of the Year 2011-2013 Top in the UK for student experience Fourth university in the UK and top in Scotland (National Student Survey 2012) We invite research leaders and ambitious early career researchers to join us in leading and driving research in key inter-disciplinary themes. Please see www.hw.ac.uk/researchleaders for further information and how to apply. Heriot-Watt University is a Scottish charity registered under charity number SC000278. -- 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.
Re: [gmx-users] Atomistic Simulation
On 12/3/13 6:17 AM, Hardy, Adam wrote: I've just started doing atomistic simulations over the last few weeks as well and can share what I've learned so far. I have been using 'automated topology builder'. It only uses the gromos 53a6 forcefield so eliminates the choice if you want to use it. ATB generates the pdb and itp files for you. There are a lot of molecules already on there or you can submit you're own using a java script molecule builder. There may well be other ways to do this but I haven't found them yet. There are many other sources of parameters for simple molecules like these. 1. http://virtualchemistry.org/ 2. https://www.paramchem.org/ 3. AmberTools can be used to build (using xLeap) and create topologies (antechamber) for just about anything under GAFF There are plenty of other sources. The most important choice is constructing a model that accurately reproduces quantities of interest. It may take several attempts using several force fields to find the right one, or you may have to derive your own model from scratch if none of the existing ones is sufficient. On 3 Dec 2013 10:14, panzu wrote: Hello to everybody, I am new in atomistic simulations and a have some doubts about how to do it. I wanna simulate a mixture of Cyclohexane, Toluene and Dodecane. My questions are, ¿Where do I get the pdb files of these molecules from? and ¿How do I know which force field I should choose in pdb2gmx in order to make the itp file? You don't need pdb2gmx at all here. The topology should be manually constructed; pdb2gmx is not useful in cases like these. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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.
Re: [gmx-users] Atomistic Simulation
I've just started doing atomistic simulations over the last few weeks as well and can share what I've learned so far. I have been using 'automated topology builder'. It only uses the gromos 53a6 forcefield so eliminates the choice if you want to use it. ATB generates the pdb and itp files for you. There are a lot of molecules already on there or you can submit you're own using a java script molecule builder. There may well be other ways to do this but I haven't found them yet. On 3 Dec 2013 10:14, panzu wrote: Hello to everybody, I am new in atomistic simulations and a have some doubts about how to do it. I wanna simulate a mixture of Cyclohexane, Toluene and Dodecane. My questions are, ¿Where do I get the pdb files of these molecules from? and ¿How do I know which force field I should choose in pdb2gmx in order to make the itp file? Thanks in advance, Panzu -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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. - Sunday Times Scottish University of the Year 2011-2013 Top in the UK for student experience Fourth university in the UK and top in Scotland (National Student Survey 2012) We invite research leaders and ambitious early career researchers to join us in leading and driving research in key inter-disciplinary themes. Please see www.hw.ac.uk/researchleaders for further information and how to apply. Heriot-Watt University is a Scottish charity registered under charity number SC000278. -- 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.
[gmx-users] Atomistic Simulation
Hello to everybody, I am new in atomistic simulations and a have some doubts about how to do it. I wanna simulate a mixture of Cyclohexane, Toluene and Dodecane. My questions are, ¿Where do I get the pdb files of these molecules from? and ¿How do I know which force field I should choose in pdb2gmx in order to make the itp file? Thanks in advance, Panzu -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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.
