Re: [gmx-users] CHARMM36 force field available for GROMACS
Nice trick - I didn't realise you could chain and group sed regular
expressions that way!
Neither did I know pdb2gmx had an .arn database.
That's two things I've learned... Can I go home now? :-D
Mark
On Mar 10, 2014 7:32 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
cat $pdbfile | sed 's/TIP3/SOL /' | sed 's/ OH2 SOL/ OW SOL/' | sed 's/
H1 SOL/ HW1 SOL/' | sed 's/ H2 SOL/ HW2 SOL/' | sed 's/ SOD SOD/ NA NA
/g
' | sed 's/ CLA CLA/ CL CL /g'
Something like this in one command?:
sed 's/TIP3/SOL /;/SOL/{s/OH2/OW /;s/H1 /HW1/;s/H2 /HW2/;};s/SOD/NA
/g;s/CLA/CL /g;' $pdbfile
Cheers,
Tsjerk
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Re: [gmx-users] parameters problem
On 3/10/14, 2:45 AM, Nidhi Katyal wrote: Thank you Mark and Justin. Now, I have carried out simulations using PME electrostatics and using all other parameters (except gromos 96 43a1 ff used) as suggested in http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/ The protein is not loosing its structure now. But the problem is if I carry out simulations in the presence of experimentally known stabiliser generated using ProDrg (keeping all the parameters same while simulating both in the presence and absence of stabiliser), the partial loss of secondary structure is observed in the presence of stabilizer relative to the case in its absence at 350K thereby implying simulations going against experimental observations (although slight stabilization was observed at 300K). Simulations were repeated twice with two different force fields. However if I use above em,pr,full parameters with cut-off electrostatics, although secondary structure is lost in the initial stages but I could clearly see the stabilization behaviour of additive in terms of secondary structure retainment till longer time. Is this observation a matter of chance- reliable or not? What could be the possible reason for not observing such stabilization with better parameters? Cutoff electrostatics are horribly inaccurate. The fact that you conveniently see what you hope to when using a plain cutoff is likely by chance. The bigger issue is the use of PRODRG parameters. As I have said numerous times on this list, the parameters it produces are demonstrably inaccurate and require reparametrization. http://pubs.acs.org/doi/abs/10.1021/ci100335w -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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.
Re: [gmx-users] Performing protein-ligand GROMACS MD under pH 5 conditions
It depends. Google knows a fair bit about constant pH md simulation Mark On Mon, Mar 10, 2014 at 10:29 AM, MUSYOKA THOMMAS mutemibiochemis...@gmail.com wrote: Dear Users, I am doing MD simulations involving lysosomal proteins catalases and small organic compounds and would be glad to know how I can achieve this under a pH=5 environment. Thank uou -- 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.
[gmx-users] Problem in extending simulation with state.cpt while changing number of cores
Hello all, I was simulating a mixture of water and carbon-di-oxide for 20ns in one node with 32 cores. After completion of 20ns run' I extended it for further 15ns with tpbconv as follows- tpbconv -s 20ns_old.tpr -extend 15000 -o 15ns_new.tpr -cpi state.cpt mdrun -s 15ns_new.tpr -o last_15ns.trr The last 15ns run was carried out in one node with 12 cores. When I plot coulomb potential energy (short range) for whole 35ns trajectory, I observe a sharp rise at the extention time (i.e at the begining of last 15ns run). This sharp rise is not observed if the number of cores are kept same during extension. Any comments/suggestions on this observation will be beneficial to me. Thanks in advance. Bappa Ghosh Project Student .. C/O -Dr Sudip Roy Scientist, CSIR-National Chemical Laboratory, Pune-411008,India -- 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] Problem in extending simulation with state.cpt while changing number of cores
Please always report at least your GROMACS version! tpbconv does not take a -cpi argument, so if that is really your command line, then it is not doing what you think it is doing. Then mdrun has no option but to re-start from the only frame it knows about - the one from which you originally started. Mark On Mon, Mar 10, 2014 at 5:23 PM, Bappa Ghosh ab54...@gmail.com wrote: Hello all, I was simulating a mixture of water and carbon-di-oxide for 20ns in one node with 32 cores. After completion of 20ns run' I extended it for further 15ns with tpbconv as follows- tpbconv -s 20ns_old.tpr -extend 15000 -o 15ns_new.tpr -cpi state.cpt mdrun -s 15ns_new.tpr -o last_15ns.trr The last 15ns run was carried out in one node with 12 cores. When I plot coulomb potential energy (short range) for whole 35ns trajectory, I observe a sharp rise at the extention time (i.e at the begining of last 15ns run). This sharp rise is not observed if the number of cores are kept same during extension. Any comments/suggestions on this observation will be beneficial to me. Thanks in advance. Bappa Ghosh Project Student .. C/O -Dr Sudip Roy Scientist, CSIR-National Chemical Laboratory, Pune-411008,India -- 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] parameters problem
To test swiss param parameters, I have generated *.pdb and *.itp files from it. In the genbox command, I have used -ci *.pdb -nmol 2. I have included *.itp in the topology as: ; Include Position restraint file ;#ifdef POSRES ;#include posre.itp ;#endif ;Include ligand topology #include ligand.itp ; Include water topology #include charmm27.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include charmm27.ff/ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 LIG 2 SOL 12904 But after I run grompp command, I get following error: Fatal error: Syntax error - File ligand.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes Please help me rectify the problem of the order getting violated although same worked for topology generated by PRODRG. Thanks in advance. On Mon, Mar 10, 2014 at 10:06 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/10/14, 8:21 AM, Nidhi Katyal wrote: Thanks Justin. I would also like to know the reliability of parameters generated using swiss param. I have no personal experience with it. My rule is to never trust anything from a black-box server without verifying it and assessing any information about penalties, deviations, etc. that it provides. -Justin On Mon, Mar 10, 2014 at 3:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/10/14, 2:45 AM, Nidhi Katyal wrote: Thank you Mark and Justin. Now, I have carried out simulations using PME electrostatics and using all other parameters (except gromos 96 43a1 ff used) as suggested in http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ gmx-tutorials/lysozyme/ The protein is not loosing its structure now. But the problem is if I carry out simulations in the presence of experimentally known stabiliser generated using ProDrg (keeping all the parameters same while simulating both in the presence and absence of stabiliser), the partial loss of secondary structure is observed in the presence of stabilizer relative to the case in its absence at 350K thereby implying simulations going against experimental observations (although slight stabilization was observed at 300K). Simulations were repeated twice with two different force fields. However if I use above em,pr,full parameters with cut-off electrostatics, although secondary structure is lost in the initial stages but I could clearly see the stabilization behaviour of additive in terms of secondary structure retainment till longer time. Is this observation a matter of chance- reliable or not? What could be the possible reason for not observing such stabilization with better parameters? Cutoff electrostatics are horribly inaccurate. The fact that you conveniently see what you hope to when using a plain cutoff is likely by chance. The bigger issue is the use of PRODRG parameters. As I have said numerous times on this list, the parameters it produces are demonstrably inaccurate and require reparametrization. http://pubs.acs.org/doi/abs/10.1021/ci100335w -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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
Re: [gmx-users] parameters problem
Probably you will see that your ligand.itp has an [atomtypes] entry as well as a [molecule] entry, and the former cannot follow any instance of the latter. Such an .itp file must be #included to create the first molecule. You have your protein [molecule] above the #include ligand.itp at the moment, which would cause this problem. Mark On Mon, Mar 10, 2014 at 7:09 PM, Nidhi Katyal nidhikatyal1...@gmail.comwrote: To test swiss param parameters, I have generated *.pdb and *.itp files from it. In the genbox command, I have used -ci *.pdb -nmol 2. I have included *.itp in the topology as: ; Include Position restraint file ;#ifdef POSRES ;#include posre.itp ;#endif ;Include ligand topology #include ligand.itp ; Include water topology #include charmm27.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include charmm27.ff/ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 LIG 2 SOL 12904 But after I run grompp command, I get following error: Fatal error: Syntax error - File ligand.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes Please help me rectify the problem of the order getting violated although same worked for topology generated by PRODRG. Thanks in advance. On Mon, Mar 10, 2014 at 10:06 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/10/14, 8:21 AM, Nidhi Katyal wrote: Thanks Justin. I would also like to know the reliability of parameters generated using swiss param. I have no personal experience with it. My rule is to never trust anything from a black-box server without verifying it and assessing any information about penalties, deviations, etc. that it provides. -Justin On Mon, Mar 10, 2014 at 3:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/10/14, 2:45 AM, Nidhi Katyal wrote: Thank you Mark and Justin. Now, I have carried out simulations using PME electrostatics and using all other parameters (except gromos 96 43a1 ff used) as suggested in http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ gmx-tutorials/lysozyme/ The protein is not loosing its structure now. But the problem is if I carry out simulations in the presence of experimentally known stabiliser generated using ProDrg (keeping all the parameters same while simulating both in the presence and absence of stabiliser), the partial loss of secondary structure is observed in the presence of stabilizer relative to the case in its absence at 350K thereby implying simulations going against experimental observations (although slight stabilization was observed at 300K). Simulations were repeated twice with two different force fields. However if I use above em,pr,full parameters with cut-off electrostatics, although secondary structure is lost in the initial stages but I could clearly see the stabilization behaviour of additive in terms of secondary structure retainment till longer time. Is this observation a matter of chance- reliable or not? What could be the possible reason for not observing such stabilization with better parameters? Cutoff electrostatics are horribly inaccurate. The fact that you conveniently see what you hope to when using a plain cutoff is likely by chance. The bigger issue is the use of PRODRG parameters. As I have said numerous times on this list, the parameters it produces are demonstrably inaccurate and require reparametrization. http://pubs.acs.org/doi/abs/10.1021/ci100335w -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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
Re: [gmx-users] Problem in extending simulation with state.cpt while changing number of cores
Thanks Mark for your reply, I am using gromacs version 4.6.3 with single precision. Also I used state.cpt in mdrun , not in the tpbconv. I apologise for my typing mistake. So the command line was as follows- tpbconv -s 20ns_old.tpr -extend 15000 -o 15ns_new.tpr mdrun -s 15ns_new.tpr -o last_15ns.trr -cpi state.cpt On Mon, Mar 10, 2014 at 10:11 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Please always report at least your GROMACS version! tpbconv does not take a -cpi argument, so if that is really your command line, then it is not doing what you think it is doing. Then mdrun has no option but to re-start from the only frame it knows about - the one from which you originally started. Mark On Mon, Mar 10, 2014 at 5:23 PM, Bappa Ghosh ab54...@gmail.com wrote: Hello all, I was simulating a mixture of water and carbon-di-oxide for 20ns in one node with 32 cores. After completion of 20ns run' I extended it for further 15ns with tpbconv as follows- tpbconv -s 20ns_old.tpr -extend 15000 -o 15ns_new.tpr -cpi state.cpt mdrun -s 15ns_new.tpr -o last_15ns.trr The last 15ns run was carried out in one node with 12 cores. When I plot coulomb potential energy (short range) for whole 35ns trajectory, I observe a sharp rise at the extention time (i.e at the begining of last 15ns run). This sharp rise is not observed if the number of cores are kept same during extension. Any comments/suggestions on this observation will be beneficial to me. Thanks in advance. Bappa Ghosh Project Student .. C/O -Dr Sudip Roy Scientist, CSIR-National Chemical Laboratory, Pune-411008,India -- 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. -- 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] about insane.py script on martini website.
I want to generate a .gro file for a coarse-grained model of a single DLPC lipid. I learned I can used the insane.py script on martini website. This is the input command I used: python insane.py -d 1 -x 1 -y 1 -z 3 -l DLPC -asym 1 -sol 0 -o dlpc.gro Yes I get an output but I don't think I have the right structure. Thanks. :) -- View this message in context: http://gromacs.5086.x6.nabble.com/about-insane-py-script-on-martini-website-tp5015065.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.
