[gmx-users] free energy landscape question
Hi, I am trying to use g_sham to obtain free energy landscape from a simulation. I can obtain the .xpm files but I want to know if there is any way of obtaining the actual histogram (in a form of a ASCII matrix vith numerical values) to use it in some other plotting program to draw contour lines plots of the surface Many thanks, Andrei -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] umbrella sampling-Bimodal Histograms
I took initial 300 as equilibration,Now it seems fine. Thank you .. On Tue, Jun 22, 2010 at 9:21 AM, chris.ne...@utoronto.ca wrote: Take that replica on the left that shows a bimodal histogram. Now plot a time series of the displacement: x-axis = time and y-axis = displacement along reaction coord. Is it jumping back and forth between two regions of sampling? Probably not... more likely it starts near one maximum and transitions to another maximum. If this is true then it simply means that you have not equilibrated enough. Run longer and cut some of the initial sampling. Chris. -- original message -- I am doing US . Yes, histograms of population densities along the reaction coordinate. Please find the pull settings. Sampled for 800ps.(nsteps = 40). Pull_init will vary for each frame, depends on the window spacing. pull = umbrella pull_geometry= position pull_dim = N N Y pull_start = no pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = U_ref pull_pbcatom0= 0 pull_group1 = r_C1 pull_pbcatom1= 0 pull_init1 = 0 0 0.1 pull_k1 = 1000 pull_rate1 = 0 pull_vec1= 0 0 0 Please check this link for my histograms https://docs.google.com/fileview?id=0B1PyTWWGrqt6MDU3NWYwMGUtNjY5Zi00NDBmLWE0YzMtYTNjODVlOGFlNWVlhl=en I would greatly appreciate our suggestions. Thank you, -Aswathy On Mon, Jun 21, 2010 at 8:14 PM, chris.neale at utoronto.ca wrote: Please clarify: Are doing SMD or are you doing US? If you're doing SMD then you should not be using WHAM and you should not really be able to generate any sampling histograms. Are the histograms that you are referring to population densities of the sampling along your reaction coordinate? My guess -- if you're doing US -- is that you have some incorrect pull group settings. Bimodal distributions are indeed possible, but should require very long sampling times to achieve, and I doubt that you are at those times yet. Your Fc is fine. Post your pull settings. Chris. -- original message -- When i did the Umbrella sampling of frames from an SMD (of ligand transport), I am getting bimodal histograms in some cases. Do you think this is because , the force constant that i used is very low (i used pull_k1=1000).? Are these bimodal peaks may cause any deviation in my PMF result? Do I need to repeat the sampling again with another pull_k1 value(higher value)? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Aswathy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] fcstep value for shell particles
Dear all, I am trying to perform a simulation with polarizable model using Drude shell particle approach. What should be the optimum value of fcstep if my shell particle has zero mass? As far as I can understand, the default value for fcstep is 0, but can't understand what does it mean from the computational point of view. Let say, what should be fcstep value if one would like to run SW water model by van Maaren and van der Spoel? Many thanks in advance, Mikhail = Dr Mikhail Stukan Schlumberger Dhahran Carbonate Research Center, Dhahran Techno Valley - KFUPM, P.O. Box 39011, Dammam / Doha Camp 31942, Kingdom of Saudi Arabia Tel: +966 3 331 0300 ext 6182 Fax:+966 3 330 0845 mstu...@slb.commailto:mstu...@slb.com = Dr Mikhail Stukan Schlumberger Dhahran Carbonate Research Center, Dhahran Techno Valley - KFUPM, P.O. Box 39011, Dammam / Doha Camp 31942, Kingdom of Saudi Arabia Tel: +966 3 331 0300 ext 6182 Fax:+966 3 330 0845 mstu...@slb.commailto:mstu...@slb.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] fcstep value for shell particles
Hi, fcstep is only relevant for flexible constraints (hence the fc in the step). It does not affect shells. Berk From: mstu...@slb.com To: gmx-users@gromacs.org Date: Tue, 22 Jun 2010 12:25:29 +0200 Subject: [gmx-users] fcstep value for shell particles Dear all, I am trying to perform a simulation with polarizable model using Drude shell particle approach. What should be the optimum value of fcstep if my shell particle has zero mass? As far as I can understand, the default value for fcstep is 0, but can’t understand what does it mean from the computational point of view. Let say, what should be fcstep value if one would like to run SW water model by van Maaren and van der Spoel? Many thanks in advance, Mikhail = Dr Mikhail Stukan Schlumberger Dhahran Carbonate Research Center, Dhahran Techno Valley - KFUPM, P.O. Box 39011, Dammam / Doha Camp 31942, Kingdom of Saudi Arabia Tel: +966 3 331 0300 ext 6182 Fax:+966 3 330 0845 mstu...@slb.com = Dr Mikhail Stukan Schlumberger Dhahran Carbonate Research Center, Dhahran Techno Valley - KFUPM, P.O. Box 39011, Dammam / Doha Camp 31942, Kingdom of Saudi Arabia Tel: +966 3 331 0300 ext 6182 Fax:+966 3 330 0845 mstu...@slb.com _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] dgdl.xvg file
Hi, Is there command in .mdp to adjust of frequency to write dg/dlamda to dGdL.xvg file? I do mdrun for 100 steps, so I get 100 dg/dl in dgdl.xvg file while I want to change output to write 1000 dgdl in dGdL.xvg file. How can I do? thaks in advance, Afsaneh Maleki -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] OPLS-AA topologies for ATP
Hi, Does anyone have OPLS-AA topologies for ATP? Thanks, Efrat-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem while removing extra waters from a simulation box, simulation explodes thereafter
Hi I have run a lipid bilayer simulation, which has too much water in it and too few lipids (small bilayer patch, ~ 80 waters per lipid). I have used genconf to multiply the system in the xy direction to increase system size, and then removed water which is z8 angstroms and z92 angstroms using vmd to decrease my system size and remove unrequired water. After I run editconf on the truncated system getting it to the right box size, the energy minimization keeps exploding on me with lincs errors? I think this is because my (0,0,0) does not coincide with one corner of the simulation box. Or is is something else? In either case, how can this be fixed -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RE:Multiple chain ID's
Hello again, I am still working on gromacs sims on the side of wet lab work. In any case, I am still at the same point as almost several weeks back. I can take my pdb file with 5 chain IDs A-C and generate a .top and .gro file, with appropriate box (which can just be pasted at the top of the file I believe) along with the .itps for each chain. I then run an energy minimization in vacuo and it works fine, converging in 800-850 steps at 0.002 ps each I then add waters, and ions (K+, Ca2+, Mg2+, Na+ and Cl-)and generate the larger 37 MB pdb file. From this, I make_ndx , and additionally specify the residues for each chain, plus the ions, with Ca2+ in a seperate file (Protein_A-G). Now when I do a simple EM with steep, it say converged in 10-20 cycles, with a rather large force and Potential Energy = 1.9811578e+20. When I take just the protein part of the output, I find the terminal residues from each chain try to form a bond (at 10-30 Angstroms away) with the next chein, and from there the system explodes. So, How do I force a restraint, or something in gromacs which will keep the varied chains seperate, and from trying to converge or fix a gap which does not exist in a chain. I use an index file I checked all .itp files and no bonds are specified between the terminal ends I even tried staying with a .pdb file the whole time instead of .gro, but the pdb2gmx always adds an extra 4000 atoms(out of 553257) which I can not account for, as my starting .pdb has all hydrogens, etc. Basically, I just want to run a MD between a three chain and two chain protein set to observe differences upon binding, and plot the varied energy changes, along with different pharmaceuticals, etc. to compare differences,and a visualization of the movements involved, as one of the two proteins contains a number of flexible loops, etc...thus visualizatio of movement would be very helpful in illucidation of the action of varied compounds...ANd I already now read the manual 2 x it don't say much about my problem, and the two suggestions out of the 200 posts in the e-mails say use an index file, and check your .itp files for cositency. Any help or suggestions are appriciated. Sincerely, Stephan Lloyd Watkins -- GMX.ch - Schweizer FreeMail-Dienst mit über 800.000 Mitgliedern E-Mail mehr! Kostenlos: http://portal.gmx.net/de/go/chfreemail -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] RE:Multiple chain ID's
lloyd riggs wrote: Hello again, I am still working on gromacs sims on the side of wet lab work. In any case, I am still at the same point as almost several weeks back. I can take my pdb file with 5 chain IDs A-C and generate a .top and .gro file, with appropriate box (which can just be pasted at the top of the file I believe) along with the .itps for each chain. The box vectors are placed at the *bottom* of a .gro file. Do be careful about manually setting a box. If your coordinates are not positioned appropriately and have not been given sufficient solute-box space, then you might see weird behavior. Instead of manually hacking the box, use editconf - that's its purpose. I then run an energy minimization in vacuo and it works fine, converging in 800-850 steps at 0.002 ps each Just FYI, EM is run in steps, not time units. I then add waters, and ions (K+, Ca2+, Mg2+, Na+ and Cl-)and generate the larger 37 MB pdb file. From this, I make_ndx , and additionally specify the residues for each chain, plus the ions, with Ca2+ in a seperate file (Protein_A-G). Now when I do a simple EM with steep, it say converged in 10-20 cycles, with a rather large force and Potential Energy = 1.9811578e+20. When I take just the protein part of the output, I find the terminal residues from each chain try to form a bond (at 10-30 Angstroms away) with the next chein, and from there the system explodes. There is no bond formation, that's just a visualization artifact from an exploding system. Is your box size sufficiently large to avoid spurious PBC interactions? Where does the system start to explode? Any LINCS warnings? These will point you to the part of the structure where the geometry starts to fail. http://www.gromacs.org/Documentation/Terminology/Blowing_Up How did you produce the topology? Did you use pdb2gmx -merge? Did you specify the appropriate termini? It sounds to me like mdrun thinks your molecules should be continuous peptide chains rather than separate proteins. So, How do I force a restraint, or something in gromacs which will keep the varied chains seperate, and from trying to converge or fix a gap which does not exist in a chain. That depends on your answer to my question about pdb2gmx. Topologically-distinct structures should not do this, and there is no way to enforce a restraint to work around a severely broken system. I use an index file I checked all .itp files and no bonds are specified between the terminal ends I even tried staying with a .pdb file the whole time instead of .gro, but the pdb2gmx always adds an extra 4000 atoms(out of 553257) which I can not account for, as my starting .pdb has all hydrogens, etc. Then you'd better figure out what's going on - pdb2gmx doesn't just add atoms for fun. Seeing your exact commands for your entire procedure and any weirdness in the output is the only way to diagnose this. What you've described sounds like nonsense. -Justin Basically, I just want to run a MD between a three chain and two chain protein set to observe differences upon binding, and plot the varied energy changes, along with different pharmaceuticals, etc. to compare differences,and a visualization of the movements involved, as one of the two proteins contains a number of flexible loops, etc...thus visualizatio of movement would be very helpful in illucidation of the action of varied compounds...ANd I already now read the manual 2 x it don't say much about my problem, and the two suggestions out of the 200 posts in the e-mails say use an index file, and check your .itp files for cositency. Any help or suggestions are appriciated. Sincerely, Stephan Lloyd Watkins -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] standard state correction of delta G from a PMF
Hello. I was wondering if anyone could explain how to convert delta G's from a PMF (generated by umbrella sampling and WHAM) into standard state values? There are some posts here on how to do this, but are too mathematical for me to figure out. I also found the same problem when reading some papers that do standard state correction. So if anyone has the time to explain this again in a more basic manner it would be appreciated. Thanks. Elio Cino -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] error in parallel mdrun
Hi all I have a ran a simulation of 64 molecules in a cubic box with side 6 nm, using nose-hoover thermostat, parinello-rahman pressure coupling, and pme. Runnin the simulation in parallel is no problem (using 16 CPUs). However when I want to run an almost identical molecule using the exact same conditions as the previous case I get the following error (below), until eventual I reduce the number of CPUs to 4 and then everything is fine. I would however like to run the simulation using more processors if anyone can give me some advise. Note the following error is from the log file. *Program mdrun, VERSION 4.0.7 Source code file: domdec.c, line: 5888 Fatal error: There is no domain decomposition for 13 nodes that is compatible with the given box and a minimum cell size of 1.25784 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] error in parallel mdrun
Gavin Melaugh wrote: Hi all I have a ran a simulation of 64 molecules in a cubic box with side 6 nm, using nose-hoover thermostat, parinello-rahman pressure coupling, and pme. Runnin the simulation in parallel is no problem (using 16 CPUs). However when I want to run an almost identical molecule using the exact same conditions as the previous case I get the following error (below), until eventual I reduce the number of CPUs to 4 and then everything is fine. I would however like to run the simulation using more processors if anyone can give me some advise. Note the following error is from the log file. *Program mdrun, VERSION 4.0.7 Source code file: domdec.c, line: 5888 Fatal error: There is no domain decomposition for 13 nodes that is compatible with the given box and a minimum cell size of 1.25784 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition* Please search the list archive for this error. There are dozens of posts, including one from just a day or two ago. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] OPLS-AA topologies for ATP
Hi, I recently made up a topology for ADP. You can probably modify it to ATP easily. I used native OPLS atom types based on the DNA parameters (http://rnp-group.genebee.msu.su/3d/ff.htm ). The charges are copied from CHARMM27. Also, there is one dihedral angle missing, again, copied from CHARMM. Please let me know if you have any question, suggestion, Cheers, Bin === In the ffoplsaa.rtp file, I added: [ ADP ] [ atoms ] PBopls_440 1.100 0 ;P O1Bopls_441 -0.900 1 ;O O2Bopls_441 -0.900 2 ;O O3Bopls_441 -0.900 3 ;O PAopls_440 1.500 4 ;P O1Aopls_441 -0.820 5 ;O2 O2Aopls_441 -0.820 6 ;O2 O3Aopls_442 -0.740 7 ;OS O5'opls_442 -0.620 8 ;OS C5'opls_443 -0.080 9 ;CT H5''opls_444 0.09010 ;HC H5' opls_444 0.09011 ;HC C4'opls_158 0.16012 ;CT H4'opls_156 0.09013 ;HC O4'opls_180 -0.50014 ;OS C1'opls_158 0.16015 ;CT H1'opls_156 0.09016 ;HC N9opls_354 -0.05017 ;NA C8opls_353 0.34018 ;CK H8opls_359 0.12019 ;H5 N7opls_352 -0.71020 ;NB C5opls_350 0.28021 ;CB C6opls_351 0.46022 ;CA N6opls_356 -0.77023 ;N2 H61opls_357 0.38024 ;H H62opls_358 0.38025 ;H N1opls_346 -0.74026 ;NC C2opls_347 0.50027 ;CQ H2opls_355 0.13028 ;H5 N3opls_348 -0.75029 ;NC C4opls_349 0.43030 ;CB C2'opls_158 0.14031 ;CT H2''opls_156 0.09032 ;HC O2'opls_171 -0.66033 ;OH H2'opls_172 0.43034 ;HO C3'opls_158 0.14035 ;CT H3'opls_156 0.09036 ;HC O3'opls_171 -0.66037 ;OS H3Topls_172 0.43038 [ bonds ] PBO3A PBO1B PBO2B PBO3B O3A PA PAO1A PAO2A PAO5' O3'H3T O5'C5' C5'C4' C4'O4' C4'C3' O4'C1' C1' N9 C1'C2' N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 N6H61 N6H62 C6 C5 C5 N7 C2'C3' C2'O2' O2'H2' C3'O3' C1'H1' C2' H2'' C3'H3' C4'H4' C5'H5' C5' H5'' C8 H8 C2 H2 N1 C6 N3 C2 C4 C5 N7 C8 === === In the ffoplsaabon.itp file, I added: ; copied from ffoplsaanr [ angletypes ] NA CT OS 1 109.500418.680 ; DNA DCY [ dihedraltypes ] ; these are again copied from ffoplsaanr NA C CM CT 3 30.35430 0.0 -30.35430 0.0 0.0 0.0 ; aromatic ring DNA DTH C CM CT HC 3 -0.77874 -2.33623 0.0 3.11498 0.0 0.0 ; aromatic ring DNA DTH HC CT CT NA 3 0.97134 2.91401 0.0 -3.88535 0.0 0.0 ; RNA NA CT CT OH 3 16.74720 -16.74720 0.0 0.0 0.0 0.0 ; RNA CM NA CT OS 3 -3.14010 -3.14010 6.28020 0.0 0.0 0.0 ; DNA DCY C NA CT OS 3 -3.14010 -3.14010 6.28020 0.0 0.0 0.0 ; DNA DCY CT OS CT NA 3 -5.23350 7.32690 6.28020 -8.37360 0.0 0.0 ; [ dihedraltypes ] ; copied from charmm O2 POS P 1 0.0 0.12553.0 O2 POS P 1 0.0 0.41842.0 OS POS P 1 0.0 0.12553.0 OS POS P 1 0.0 0.12552.0 === On Jun 22, 2010, at 5:07 AM, Efrat Noy wrote: Hi, Does anyone have OPLS-AA topologies for ATP? Thanks, Efrat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] PRODRG crash
Dear Justin, Actually, I used -d option because you said the atoms in the box must be half a bond length from the edges of box...I thought maybe this can be done by -d... With PRODRG I am unable to produce coordinate file a chain with less than three C atoms. I sketched the molecules: C-C ethane C=C Ethylene but I am getting a message: ERRDRG PRODRG does not deal with mono/di-atomic molecules. PRODRG Program terminated unsuccessfully, sorry! 1- Could you please help me with this. (actually I need structure file of ethylene in the future) 2- How can I generate structure file of repeating unit -CH2-CH2- with PRODRG. I tried the followings...and all I am getting is the above message.. :( H H | | C-C | | H H H H | | -C-C- | | H H -C-C- Moeed -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] PRODRG crash
Moeed wrote: Dear Justin, Actually, I used -d option because you said the atoms in the box must be half a bond length from the edges of box...I thought maybe this can be done by -d... My point was that you should not be using a combination of -box, -d, and -angles simultaneously. Use either -box or -d, not both, and don't use -angles. With PRODRG I am unable to produce coordinate file a chain with less than three C atoms. I sketched the molecules: C-C ethane C=C Ethylene but I am getting a message: ERRDRG PRODRG does not deal with mono/di-atomic molecules. PRODRG Program terminated unsuccessfully, sorry! 1- Could you please help me with this. (actually I need structure file of ethylene in the future) So make a 4-carbon repeat unit. It's easy to draw chains with PRODRG (but there is a limitation to the number of atoms). -Justin 2- How can I generate structure file of repeating unit -CH2-CH2- with PRODRG. I tried the followings...and all I am getting is the above message.. :( H H | | C-C | | H H H H | | -C-C- | | H H -C-C- Moeed -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] standard state correction of delta G from a PMF
Dear Elio: First, you need to convert your PMF to a free energy difference between states. That means defining a boundary between, for example, bound and unbound states. The integrate your PMF over the bound and unbound states to get two dG values, and their difference is your free energy of binding. Next for the standard state correction that is required to convert this free energy of binding into a standard state free energy of binding. This is necessary because the volume available to the unbound state affects the dG value. In the simplest case, you are going to calculate the concentration of your ligand in the unbound state and make a volume-based energetic correction to the dG value to align the dG with a 1M concentration of unbound ligand. This may be a little more complex depending on how did your simulations (US vs. FEP for example) but still the whole idea behind this is that you need to report values for dG at 1M concentration of ligand. There may be other corrections that you require, but if you're having trouble with this concept then you should move to a simple system for now. If you still have trouble, then your next post should include thinks like I tried this... but I didn't understand this specific part to make it clear that you have put in the effort here. Chris. -- original message -- Hello. I was wondering if anyone could explain how to convert delta G's from a PMF (generated by umbrella sampling and WHAM) into standard state values? There are some posts here on how to do this, but are too mathematical for me to figure out. I also found the same problem when reading some papers that do standard state correction. So if anyone has the time to explain this again in a more basic manner it would be appreciated. Thanks. Elio Cino -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Charmm without CMAP
Hi! You can choose cmap/no cmap when you run pdb2gmx. /Per Skickat från min iPhone 22 jun 2010 kl. 19:24 skrev Sai Pooja saipo...@gmail.com: Hi, I am using gromacs from the git repository which I downloaded 2 days back. Charmm has been implemented in this version. Is it possible to use the Charmm ff without CMAP with it? Regards Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] grompp fatal error Unknown bond_atomtype
Hi Users, I am experiencing the following fatal error when I try using the grompp command. grompp -f mdout.mdp -r conf.gro -p topol.top . . . --- Program grompp, VERSION 4.0.99-dev-20100409-004 Source code file: toppush.c, line: 631 Fatal error: Unknown bond_atomtype OSL . . . OSL is defined in the atomtypes.atp file located in the force field folder that I constructed. Thus, I do not understand why it is unknown. Does anybody know how to address this error? Many Thanks, Peter Huwe -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Charmm without CMAP
Thanks! On Tue, Jun 22, 2010 at 2:07 PM, Per Larsson per.lars...@sbc.su.se wrote: Hi! You can choose cmap/no cmap when you run pdb2gmx. /Per Skickat från min iPhone 22 jun 2010 kl. 19:24 skrev Sai Pooja saipo...@gmail.com: Hi, I am using gromacs from the git repository which I downloaded 2 days back. Charmm has been implemented in this version. Is it possible to use the Charmm ff without CMAP with it? Regards Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] output of the -hist option of the g_wham command
Hi all, I am trying to perform umbrella sampling along with the WHAM to get the PMF. I go over the umbrella sampling tutorial prepared by Justin. Everything seems OK to me except one point. I could not understand the output given by the hist option of the g_wham command. There, what does histogram of configurations mean? Thank you -- Ozge Engin ★☆ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] building up a long polymer chain
Hello Justin, I created structure file for a 4-carbon repeating unit as follows: HETATM1 CAA DRG 1 14.260 -4.270 0.000 1.00 20.00 C HETATM2 1HAA DRG 1 14.175 -3.426 0.530 1.00 20.00 H HETATM3 2HAA DRG 1 15.050 -4.790 0.326 1.00 20.00 H HETATM4 3HAA DRG 1 14.385 -4.045 -0.966 1.00 20.00 H HETATM5 CAB DRG 1 12.990 -5.110 0.170 1.00 20.00 C HETATM6 1HAB DRG 1 12.205 -4.581 -0.153 1.00 20.00 H HETATM7 2HAB DRG 1 12.871 -5.326 1.139 1.00 20.00 H HETATM8 CAC DRG 1 13.070 -6.410 -0.620 1.00 20.00 C HETATM9 1HAC DRG 1 13.855 -6.939 -0.297 1.00 20.00 H HETATM 10 2HAC DRG 1 13.189 -6.194 -1.589 1.00 20.00 H HETATM 11 CAD DRG 1 11.800 -7.250 -0.450 1.00 20.00 C HETATM 12 1HAD DRG 1 11.885 -8.094 -0.980 1.00 20.00 H HETATM 13 2HAD DRG 1 11.675 -7.475 0.516 1.00 20.00 H HETATM 14 3HAD DRG 1 11.010 -6.730 -0.776 1.00 20.00 H I renamed the atoms and removed one hydrogen atoms from both ends to get repeating unit. CH2CH2, 1- I am not able to produce the repeating unit C2H4 in PRODRG. It adds the third H automatically. I dont know anyother way but removing the third H from structure file by hand.. Then I mesaured the C1 To C4 distance which is 0.388 A. editconf -f prodrg.pdb -o prodrg.gro -box 0.388 -bt cubic 12 1DRG C11 0.208 0.006 0.242 1DRGH112 0.158 0.010 0.328 1DRGH123 0.149 -0.030 0.170 1DRG C24 0.255 0.148 0.203 1DRGH215 0.305 0.143 0.116 1DRGH226 0.314 0.184 0.274 1DRG C37 0.133 0.240 0.186 1DRGH318 0.083 0.245 0.272 1DRGH329 0.074 0.204 0.114 1DRG C4 10 0.179 0.382 0.147 1DRGH41 11 0.239 0.418 0.218 1DRGH42 12 0.230 0.378 0.060 0.38800 0.38800 0.38800 then : genconf -f prodrg.gro -o rep.gro -nbox 1 5 1 2- The problem here is that one CH2 unit with 2 H atoms is falling on the next repeating unit in the next box. i.e 4 H atoms and C atoms are overlapping... as shown below: H H H *H H* H H H | | | | | | | | C-C-C-*CC*-C-C-C | | | | | | | | H H H *H H* H H H Do you think I should use -d option? Please guide me.. Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] building up a long polymer chain
Moeed wrote: Hello Justin, I created structure file for a 4-carbon repeating unit as follows: HETATM1 CAA DRG 1 14.260 -4.270 0.000 1.00 20.00 C HETATM2 1HAA DRG 1 14.175 -3.426 0.530 1.00 20.00 H HETATM3 2HAA DRG 1 15.050 -4.790 0.326 1.00 20.00 H HETATM4 3HAA DRG 1 14.385 -4.045 -0.966 1.00 20.00 H HETATM5 CAB DRG 1 12.990 -5.110 0.170 1.00 20.00 C HETATM6 1HAB DRG 1 12.205 -4.581 -0.153 1.00 20.00 H HETATM7 2HAB DRG 1 12.871 -5.326 1.139 1.00 20.00 H HETATM8 CAC DRG 1 13.070 -6.410 -0.620 1.00 20.00 C HETATM9 1HAC DRG 1 13.855 -6.939 -0.297 1.00 20.00 H HETATM 10 2HAC DRG 1 13.189 -6.194 -1.589 1.00 20.00 H HETATM 11 CAD DRG 1 11.800 -7.250 -0.450 1.00 20.00 C HETATM 12 1HAD DRG 1 11.885 -8.094 -0.980 1.00 20.00 H HETATM 13 2HAD DRG 1 11.675 -7.475 0.516 1.00 20.00 H HETATM 14 3HAD DRG 1 11.010 -6.730 -0.776 1.00 20.00 H I renamed the atoms and removed one hydrogen atoms from both ends to get repeating unit. CH2CH2, 1- I am not able to produce the repeating unit C2H4 in PRODRG. It adds the third H automatically. I dont know anyother way but removing the third H from structure file by hand.. Then I mesaured the C1 To C4 distance which is 0.388 A. editconf -f prodrg.pdb -o prodrg.gro -box 0.388 -bt cubic 12 1DRG C11 0.208 0.006 0.242 1DRGH112 0.158 0.010 0.328 1DRGH123 0.149 -0.030 0.170 1DRG C24 0.255 0.148 0.203 1DRGH215 0.305 0.143 0.116 1DRGH226 0.314 0.184 0.274 1DRG C37 0.133 0.240 0.186 1DRGH318 0.083 0.245 0.272 1DRGH329 0.074 0.204 0.114 1DRG C4 10 0.179 0.382 0.147 1DRGH41 11 0.239 0.418 0.218 1DRGH42 12 0.230 0.378 0.060 0.38800 0.38800 0.38800 then : genconf -f prodrg.gro -o rep.gro -nbox 1 5 1 2- The problem here is that one CH2 unit with 2 H atoms is falling on the next repeating unit in the next box. i.e 4 H atoms and C atoms are overlapping... as shown below: H H H *H H* H H H | | | | | | | | C-C-C-*CC*-C-C-C | | | | | | | | H H H *H H* H H H Do you think I should use -d option? As I've said twice now, use either -box or -d to set an appropriately-sized unit cell. If you've measured a C...C distance of 0.388 nm, you've left no space for the bond that will occur to the next unit, so naturally you're seeing overlap. You've simply made your box too small. -Justin Please guide me.. Thanks -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] free energy landscape question
Hi, I am trying to use g_sham to obtain free energy landscape from a simulation. I can obtain the .xpm files but I want to know if there is any way of obtaining the actual histogram (in a form of a ASCII matrix vith numerical values) to use it in some other plotting program to draw contour lines plots of the surface Many thanks, Andrei -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] grompp fatal error Unknown bond_atomtype
There's lots of information in the gromacs manual to show that the .atp file is not the only file that you must modify. My most important suggestion to you is that you should read the entire manual, possibly twice, before attempting to build new molecules. Gromacs manual, page 96: 5.3.1Atoms A number of static properties are assigned to the atom types in the GROMACS force field: Type, Mass, Charge, and ? (see Table 5.2 The mass is listed in ff???.atp (see 5.2.1), whereas the charge is listed in ff???.rtp (.rtp = residue topology parameter file, see 5.6.1). This implies that the charges are only defined in the building blocks of amino acids or user defined building blocks. When generating a topology (*.top) using the pdb2gmx program the information from these files is combined. Then on page 97: In the file ff???bon.itp you can add bonded parameters. If you want to include parameters for new atom types, make sure you define this new atom type in ff???.atp as well. Then on page 120: For each force field there a five files which are only used by pdb2gmx. These are: the residue database (.rtp, see 5.6.1) the hydrogen database (.hdb, see 5.6.2), two termini databases (.tdb, see 5.6.3) and the atom type database (.atp) which contains only the masses. I'm not going to post a detailed account of how to add an atom because it is key for you to fully understand what all of the forcefield files are doing if you are going to do something like create a new atom type. The information is all in the manual though, and search exotic species on the wiki, although lots of links there are still broken after the migration to a new wiki type. By the way, you didn't post nearly enough information! You are trying to parameterize a new molecule and you got an error and the only thing that you posted was the error message . you're much more likely to get good help if you make it easier for everybody else to help you. Chris -- original message -- Hi Users, I am experiencing the following fatal error when I try using the grompp command. grompp -f mdout.mdp -r conf.gro -p topol.top . . . --- Program grompp, VERSION 4.0.99-dev-20100409-004 Source code file: toppush.c, line: 631 Fatal error: Unknown bond_atomtype OSL . . . OSL is defined in the atomtypes.atp file located in the force field folder that I constructed. Thus, I do not understand why it is unknown. Does anybody know how to address this error? Many Thanks, Peter Huwe -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: chain ids (2)
Dear All, I am re-posting with some replies to my first message. the cell demensions for .gro files are at the bottomn, you know, you right. There at the top for .pdb file, and it is just a unit cell, and not very trivial to center graphically. And when you answere somones question like below, you should read what they stated first. I then run an energy minimization in vacuo and it works fine, converging in 800-850 steps at 0.002 ps each Just FYI, EM is run in steps, not time units. I used the term step even? Correcting every little thing to the point of overdoing it makes people not want to talk to you, especially when it does not solve or answere the problem. I'm not your dad, you don't have to prove something to me, I know how well you know the software. In any case, It is obvious my problem is the system blowing up, visually it is only the terminal residues from each chain, and from runs such as lincs warnings, it is the same atoms in these terminal residues, which are the problem. Basically, gromacs, as I said, can not keep the chain ids, even when I use an index file, and beforehand, yes I checked all the .itp, .ndx etc to make sure atoms are all properly coordinated. The extra atoms, I can acount for a couple, such as the extra hydrogen at terminal end, and yes even the interactive use of pdb2gmx as a starting point for the topology still gives problems. Timing wise, it seems to break down when I add waters, when I run this alone, it starts to explode. I have tried step by step making of .top files as well, and re-adding chain IDs after a crash, etc...or just following a step by step proceedure from scrath again several times. As I had stated, if the system only has the 5 proteins, and no solvent, it has no problem, but then this is usually the first run after switching from a pdb to .gro file, whith the .pdb generating the .top with it's origional chain IDs. SAnd like I said, any helpful suggestions are appriciated. lloyd riggs wrote: Hello again, I am still working on gromacs sims on the side of wet lab work. In any case, I am still at the same point as almost several weeks back. I can take my pdb file with 5 chain IDs A-C and generate a .top and .gro file, with appropriate box (which can just be pasted at the top of the file I believe) along with the .itps for each chain. The box vectors are placed at the *bottom* of a .gro file. Do be careful about manually setting a box. If your coordinates are not positioned appropriately and have not been given sufficient solute-box space, then you might see weird behavior. Instead of manually hacking the box, use editconf - that's its purpose. I then run an energy minimization in vacuo and it works fine, converging in 800-850 steps at 0.002 ps each Just FYI, EM is run in steps, not time units. I then add waters, and ions (K+, Ca2+, Mg2+, Na+ and Cl-)and generate the larger 37 MB pdb file. From this, I make_ndx , and additionally specify the residues for each chain, plus the ions, with Ca2+ in a seperate file (Protein_A-G). Now when I do a simple EM with steep, it say converged in 10-20 cycles, with a rather large force and Potential Energy = 1.9811578e+20. When I take just the protein part of the output, I find the terminal residues from each chain try to form a bond (at 10-30 Angstroms away) with the next chein, and from there the system explodes. There is no bond formation, that's just a visualization artifact from an exploding system. Is your box size sufficiently large to avoid spurious PBC interactions? Where does the system start to explode? Any LINCS warnings? These will point you to the part of the structure where the geometry starts to fail. http://www.gromacs.org/Documentation/Terminology/Blowing_Up How did you produce the topology? Did you use pdb2gmx -merge? Did you specify the appropriate termini? It sounds to me like mdrun thinks your molecules should be continuous peptide chains rather than separate proteins. So, How do I force a restraint, or something in gromacs which will keep the varied chains seperate, and from trying to converge or fix a gap which does not exist in a chain. That depends on your answer to my question about pdb2gmx. Topologically-distinct structures should not do this, and there is no way to enforce a restraint to work around a severely broken system. I use an index file I checked all .itp files and no bonds are specified between the terminal ends I even tried staying with a .pdb file the whole time instead of .gro, but the pdb2gmx always adds an extra 4000 atoms(out of 553257) which I can not account for, as my starting .pdb has all hydrogens, etc. Then you'd better figure out what's going on - pdb2gmx doesn't just add atoms for fun. Seeing your exact commands for your entire procedure and any weirdness in the output is the only way to diagnose this. What you've described sounds like nonsense. -Justin Basically,
