Re: [gmx-users] Energy minimization result problem
Hello I am new user of gromacs. I am using gromacs 4.6.3 I wanted to minimize the energy of a protein. Before energy minimization the prockeck result for Ramachandran plot was 89% in allowed region but after energy minimization the result become worse i.e. 87%. I was performing energy minimization to refine the model. But the model become worse after that. I Model the protein using homology modeling and needed it for docking I am also doing it with different protein molecules but again the same problem occurs. I don't know that its normal or there is problem with my parameter or force field. I am also mentioning the detail of my energy minimization. The details are: Force Field Used: CHARMM27 all-atom force field Water Model: TIP3P em.mdp file is: ; VARIOUS PREPROCESSING OPTIONS = title= cpp = /lib/cpp include = define = -DFLEXIBLE ; RUN CONTROL PARAMETERS = integrator = steep ; start time and timestep in ps = tinit= 0 dt = 0.002 nsteps = 15000 ; ENERGY MINIMIZATION OPTIONS = emtol= 10 emstep = 0.1 nstcgsteep = 1000 coulombtype =pme nstenergy =10 Please help me out for this. -- View this message in context: http://gromacs.5086.x6.nabble.com/Re-Energy-minimization-result-problem-tp5015793.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] Energy minimization result problem
On 4/11/14, 7:47 AM, neha_bharty wrote: Hello I am new user of gromacs. I am using gromacs 4.6.3 I wanted to minimize the energy of a protein. Before energy minimization the prockeck result for Ramachandran plot was 89% in allowed region but after energy minimization the result become worse i.e. 87%. I was performing energy minimization to refine the model. But the model become worse after that. That's not a huge change, nor is energy minimization rigorous enough to fully refine a model. EM will probably optimize the side chains pretty well, but the backbone may require actual MD simulation to sample better conformations. The changes that take place during EM are typically very small. I Model the protein using homology modeling and needed it for docking I am also doing it with different protein molecules but again the same problem occurs. I don't know that its normal or there is problem with my parameter or force field. I am also mentioning the detail of my energy minimization. The details are: Force Field Used: CHARMM27 all-atom force field Water Model: TIP3P CHARMM36 may be a better option. The recalibration of the CMAP terms could be relevant here. See http://mackerell.umaryland.edu/CHARMM_ff_params.html to download the force field files. -Justin em.mdp file is: ; VARIOUS PREPROCESSING OPTIONS = title= cpp = /lib/cpp include = define = -DFLEXIBLE ; RUN CONTROL PARAMETERS = integrator = steep ; start time and timestep in ps = tinit= 0 dt = 0.002 nsteps = 15000 ; ENERGY MINIMIZATION OPTIONS = emtol= 10 emstep = 0.1 nstcgsteep = 1000 coulombtype =pme nstenergy =10 Please help me out for this. -- View this message in context: http://gromacs.5086.x6.nabble.com/Re-Energy-minimization-result-problem-tp5015793.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- == 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] question about xvg file
Hi Andrew, Something like: awk '!$1%16' file.xvg Cheers, Tsjerk On Apr 11, 2014 5:46 PM, Andrew Bostick andrew.bosti...@gmail.com wrote: Dear gromacs users I did a MD simulation 1 years ago. Now, I have a dist.xvg file and I have not trajectory file (xtc). Time column in dist.xvg file is as follows: 0 4 8 12 16 . . . . 24984 24988 24992 24996 25000 I want to have this column as follows: 0 16 32 64 . . . . 24936 24952 24968 24984 25000 I know If I had xtc file, I could use trjconv -dt to do my interest. Now, I have not xtc file, how to do this state? Any help will highly appreciated. -- 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] question about xvg file
Apologies... should be awk '!($1%16)' file.xvg Cheers, Tsjerk On Apr 11, 2014 6:13 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Andrew, Something like: awk '!$1%16' file.xvg Cheers, Tsjerk On Apr 11, 2014 5:46 PM, Andrew Bostick andrew.bosti...@gmail.com wrote: Dear gromacs users I did a MD simulation 1 years ago. Now, I have a dist.xvg file and I have not trajectory file (xtc). Time column in dist.xvg file is as follows: 0 4 8 12 16 . . . . 24984 24988 24992 24996 25000 I want to have this column as follows: 0 16 32 64 . . . . 24936 24952 24968 24984 25000 I know If I had xtc file, I could use trjconv -dt to do my interest. Now, I have not xtc file, how to do this state? Any help will highly appreciated. -- 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] question about xvg file
Dear Tsjerk Thanks for your quick reply. I used awk '!($1%16)' file.xvg. It is very good. Since my xvg file is large. I want to have output in new xvg file (new.xvg) instead of screen. How to do this? -- 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] question about xvg file
On 4/11/14, 1:13 PM, Andrew Bostick wrote: Dear Tsjerk Thanks for your quick reply. I used awk '!($1%16)' file.xvg. It is very good. Since my xvg file is large. I want to have output in new xvg file (new.xvg) instead of screen. How to do this? http://stackoverflow.com/questions/6674327/redirect-all-output-to-file -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] adding ATP parms to AMBER99
On 4/11/14, 1:43 PM, Stephen N. Floor wrote: Hi gromacs users - I am trying to simulate a protein-ATP complex and am trying to add parameters for ATP to the forcefield amber99sb-ildn. First off, I find it likely that someone has already done this - is there an .itp file for ATP floating around somewhere with the recommended parameters from Meagher, Redman Carlson, JCC (2003)? http://www.ncbi.nlm.nih.gov/pubmed/12759902 The .rtp and .hdb files that you would need to create the topology with pdb2gmx appear to be available from: http://bugzilla.gromacs.org/issues/721 You still need to modify ffbonded.itp and ffnonbonded.itp to use the published parameters, since they differ from those already in the force field. If not, I am trying to decide between using parms generated from PRODRG (which spits out a .itp, albeit with non-amber atom types) versus editing the ffbonded and ffnonbonded files for the forcefield to include bond, angle, and dihedral parms from Meagher 2003. Any thoughts on this? I am partial to using parameters from Meagher 2003 since they did a full QM treatment of the ligand and these are recommended by Bryce. Abort any notion of using PRODRG. The topology is of no use to you, because you literally have to change everything about it. I tried to follow previous messages in the gmx-users list on this topic, but am stuck translating dihedrals from the AMBER94 FRCMOD file to ffbonded.itp, as recommended in a previous thread (http://gromacs.5086.x6.nabble.com/Re-AMBER-force-fields-for-ATP-td4440113.html) If you can explain where you're stuck, probably someone can suggest something to help. Without knowing what stuck means, there's not much to go on :) For the AMBER94 PREP and FRCMOD files please see here: http://www.pharmacy.manchester.ac.uk/bryce/amber/ I think I could generate input files that would be properly parsed, but am looking for verification that I'm doing it correctly before conducting simulations with incorrect parameters. All that's necessary is translation between file formats (and units); there are many scripts online floating around that do this. Your approach (aside from the PRODRG tangent) is correct. The simplest test to convince yourself that everything is OK is to do a single-point energy evaluation within Gromacs and then in AMBER; if the energies are the same, the force fields are equivalent. -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] adding ATP parms to AMBER99
Hi, I have an itp. I will send it to you off list. Cheers Tom On 04/11/2014 06:43 PM, Stephen N. Floor wrote: Hi gromacs users - I am trying to simulate a protein-ATP complex and am trying to add parameters for ATP to the forcefield amber99sb-ildn. First off, I find it likely that someone has already done this - is there an .itp file for ATP floating around somewhere with the recommended parameters from Meagher, Redman Carlson, JCC (2003)? http://www.ncbi.nlm.nih.gov/pubmed/12759902 If not, I am trying to decide between using parms generated from PRODRG (which spits out a .itp, albeit with non-amber atom types) versus editing the ffbonded and ffnonbonded files for the forcefield to include bond, angle, and dihedral parms from Meagher 2003. Any thoughts on this? I am partial to using parameters from Meagher 2003 since they did a full QM treatment of the ligand and these are recommended by Bryce. I tried to follow previous messages in the gmx-users list on this topic, but am stuck translating dihedrals from the AMBER94 FRCMOD file to ffbonded.itp, as recommended in a previous thread (http://gromacs.5086.x6.nabble.com/Re-AMBER-force-fields-for-ATP-td4440113.html) For the AMBER94 PREP and FRCMOD files please see here: http://www.pharmacy.manchester.ac.uk/bryce/amber/ I think I could generate input files that would be properly parsed, but am looking for verification that I'm doing it correctly before conducting simulations with incorrect parameters. Thanks for your time. -Stephen -- Stephen N. Floor HHMI Fellow of the Helen Hay Whitney Foundation Doudna Group http://doudna.berkeley.edu -- Dr Thomas Piggot University of Southampton, UK. -- 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] multiple peptides in the same box
Hi, Justin Thank you very much! If I want 6 peptides in a same box, I revised it as follow: 1.pdb2gmx -f 1IYT.pdb -o 1IYT.gro -ignh -ter -water spce -p 1IYT.top 2.genconf -f 1IYT.gro -nbox 1 1 1 -o 1IYTlarge_box.gro -renumber -rot -maxrot 180 180 180 3.editconf -f 1IYTlarge_box.gro -o 1IYT_newbox.gro -c -d 1 -bt cubic 4.genbox -cp 1IYT_newbox.gro -nmol 5 -ci 1IYT.gro -p 1IYT.top -o 1IYT_6.gro -try 500 However, when I use VMD to check the 1IYT_6.gro, and get 12 fragments(12 proteins), actually I should get 6 fragments. http://gromacs.5086.x6.nabble.com/file/n5015805/A_4SO89OF207_N%29J7%60P%5DD3J.jpg http://gromacs.5086.x6.nabble.com/file/n5015805/_AQUOZ%6042UMR8%60%24L9%7BFKDD8.jpg How I fix it? Thank you very much! -- View this message in context: http://gromacs.5086.x6.nabble.com/multiple-peptides-in-the-same-box-tp5015754p5015805.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] multiple peptides in the same box
On 4/11/14, 9:29 PM, maggin wrote: Hi, Justin Thank you very much! If I want 6 peptides in a same box, I revised it as follow: 1.pdb2gmx -f 1IYT.pdb -o 1IYT.gro -ignh -ter -water spce -p 1IYT.top 2.genconf -f 1IYT.gro -nbox 1 1 1 -o 1IYTlarge_box.gro -renumber -rot -maxrot 180 180 180 3.editconf -f 1IYTlarge_box.gro -o 1IYT_newbox.gro -c -d 1 -bt cubic 4.genbox -cp 1IYT_newbox.gro -nmol 5 -ci 1IYT.gro -p 1IYT.top -o 1IYT_6.gro -try 500 However, when I use VMD to check the 1IYT_6.gro, and get 12 fragments(12 proteins), actually I should get 6 fragments. http://gromacs.5086.x6.nabble.com/file/n5015805/A_4SO89OF207_N%29J7%60P%5DD3J.jpg http://gromacs.5086.x6.nabble.com/file/n5015805/_AQUOZ%6042UMR8%60%24L9%7BFKDD8.jpg How I fix it? Thank you very much! Either the molecules are split across periodic boundaries (which VMD knows nothing about, so it thinks the protein segments are separate), or the use of genbox -ci -nmol has inserted fragments of molecules. You can easily check by noting the number of atoms in the coordinate file. If it is exactly 6 times a single peptide, then it's just a PBC thing. It's entirely possible that genbox fragmented the molecules; the use of -ci -nmol is not designed for multi-residue molecules. If it works, great, if not, you'll need to come up with another way to prepare the system. -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.
