[gmx-users] Regarding Minimization
*Dear all,** * *I wanted to minimize the energy of a single molecule. How emtol and emsteps I have to put to get optimised single molecule structure.* * * *Thank you** * * * *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Regarding Minimization
On 4/11/2011 5:14 PM, Ravi Kumar Venkatraman wrote: *Dear all,** * *I wanted to minimize the energy of a single molecule. How emtol and emsteps I have to put to get optimised single molecule structure.* * Set them to whatever size seems reasonable to you and leaves you with a result you want. See chapter 7 for description of the parameters. Mark * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] FEP instability
Dear all, I'm trying to FEP away a TIP4P water molecule from a water box in gmx 4.5.3, but getting a jump in dH/dlambda after some time (around 100 ps), from around -5 to -600 kJ/mol/lambda. I'm using softcore with the following parameters: sc-alpha = 0.5 sc-power = 1 sc-sigma = 0.3 delta-lambda = 0 init-lambda = 0.1 couple-lambda0 = vdw couple-lambda1 = vdw-q free-energy = yes I've also tried using sc-alpha = 0 sc-power = 0 Any clues what could go wrong? Could it be due to the virtual sites? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Shell MD
Dear sir： Thank you for reading my letter. I have a few problems in Shell MD . I do not know how to set the parameter in the*.mdp file of shell md.So I hope to obtain your help. And this is my own *.mdp file below include = define = integrator = sd tinit= 0 dt = 0.004 nsteps = 1000 simulation_part = 1 init_step= 0 comm-mode nstcomm = Linear = 100 comm-grps= System bd-fric = 1 ld-seed = 1993 emtol= 10 emstep = 0.01 niter= 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr= 10 rtpi = 0.05 nstxout = 100 nstvout = 100 nstfout = 100 nstlog = 10 nstenergy= 10 nstxtcout= 10 xtc_precision= 10 xtc-grps = energygrps = CR1 nstlist = 1 ns_type = grid pbc = xyz periodic_molecules = no rlist= 2.0 coulombtype = User rcoulomb_switch = 0.0 rcoulomb = 2.0 epsilon_r= 1 epsilon_rf = 1 vdw_type = User rvdw_switch = 0.0 rvdw = 2.0 DispCorr = No table_extension = 0 energygrp_table = CR1 CR1 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes implicit_solvent = No gb_algorithm = Still nstgbradii = 1 rgbradii = 2 gb_epsilon_solvent = 80 gb_saltconc = 0 gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 sa_surface_tension = 2.092 tcoupl = berendsen tc-grps = System tau_t= 0.3 ref_t= 800 Pcoupl = no Pcoupltype = isotropic tau_p= 1 compressibility = 6.5e-5 ref_p= 5.0 refcoord_scaling = No andersen_seed= 815131 QMMM = no QMMM-grps= QMmethod = QMMMscheme = normal QMbasis = QMcharge = QMmult = SH = CASorbitals = CASelectrons = SAon = SAoff= SAsteps = MMChargeScaleFactor = 1 bOPT = bTS = annealing= annealing_npoints= annealing_time = annealing_temp = gen_vel = yes gen_temp = 313 gen-seed = 173529 constraints = none constraint_algorithm = Lincs continuation = no Shake-SOR= no shake-tol= 1e-04 lincs_order = 4 lincs-iter = 1 lincs_warnangle = 30 morse= no energygrp_excl = nwall= 0 wall_type= 9-3 wall_r_linpot= -1 wall_atomtype= wall_density = wall_ewald_zfac = 3 pull = no disre= No disre-weighting = Conservative disre-mixed = no disre-fc = 1000 disre-tau= 0 nstdisreout = 100 orire= no orire-fc = 0 orire-tau= 0 orire-fitgrp = nstorireout = 100 dihre= no dihre-fc = 1000 free-energy = no init-lambda = 0 delta-lambda = 0 sc-alpha = 0 sc-power = 0 sc-sigma = 0.3 couple-moltype = couple-lambda0 = vdw-q couple-lambda1 = vdw-q couple-intramol = no acc-grps = accelerate = freezegrps = freezedim= cos-acceleration = 0 deform = E-x = E-xt = E-y = E-yt = E-z = E-zt = user1-grps = user2-grps = userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1= 0
[gmx-users] Shell MD
Dear sir： Thank you for reading my letter. I have a few problems in Shell MD . I do not know how to set the parameter in the*.mdp file of shell md.So I hope to obtain your help. And this is my own *.mdp file below emtol= 10 emstep = 0.01 niter= 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr= 10 rtpi = 0.05 nstxout = 100 nstvout = 100 nstfout = 100 nstlog = 10 nstenergy= 10 nstxtcout= 10 xtc_precision= 10 xtc-grps = energygrps = CR1 nstlist = 1 ns_type = grid pbc = xyz periodic_molecules = no rlist= 2.0 Could you tell me which part of the parameter should be changed for Shell MD? Your prompt attention to this letter would be highly appreciated. Thanks a lot. Liyan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Regarding Extension of the potential lookup tables
*Dear All, Could anybody tell me what is the purpose of Extension of the potential lookup tables beyond the cut-off. I have read somewhere that the sum the smallest diagnol of the box and rlist should be equal to table-extension. Please explain me the same.* *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Regarding error in ion neutralization step
Dear All Could any one help me to solve this error in gromacs 4.5.5 version. I am running dynamics on apo protein and the protein shows negative charge of -6 (after choosing OPLS-AA force filed) and when i was neutralizing the -6 with +6 and generating the genion.tpr file there it shows No such moleculetype NA+ error. But the same protein was running with out any error message in gromacs 4.0.7 version. The error message was given below. Kindly rectify the problem === [student@localhost gro]$ grompp -f em.mdp -p topol.top -c genion.gro -o genem.tpr Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 2 bonded neighbours molecule type 'SOL' --- Program grompp, VERSION 4.5.5 Source code file: toppush.c, line: 1987 Fatal error: No such moleculetype NA+ For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Regards Kirubakaran P -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Regarding error in ion neutralization step
Dear All Could any one help me to solve this error in gromacs 4.5.5 version. I am running dynamics on apo protein and the protein shows negative charge of -6 (after choosing OPLS-AA force filed) and when i was neutralizing the -6 with +6 and generating the genion.tpr file there it shows No such moleculetype NA+ error. But the same protein was running with out any error message in gromacs 4.0.7 version. The error message was given below. Kindly rectify the problem === [student@localhost gro]$ grompp -f em.mdp -p topol.top -c genion.gro -o genem.tpr Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 2 bonded neighbours molecule type 'SOL' --- Program grompp, VERSION 4.5.5 Source code file: toppush.c, line: 1987 Fatal error: No such moleculetype NA+ For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Regards Kirubakaran P -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Regarding error in ion neutralization step
On 5/11/2011 1:05 AM, kirubakaran palani wrote: Dear All Could any one help me to solve this error in gromacs 4.5.5 version. I am running dynamics on apo protein and the protein shows negative charge of -6 (after choosing OPLS-AA force filed) and when i was neutralizing the -6 with +6 and generating the genion.tpr file there it shows No such moleculetype NA+ error. But the same protein was running with out any error message in gromacs 4.0.7 version. The naming convention has changed. See share/top/oplsa.ff/ions.itp Mark The error message was given below. Kindly rectify the problem === [student@localhost gro]$ grompp -f em.mdp -p topol.top -c genion.gro -o genem.tpr Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 2 bonded neighbours molecule type 'SOL' --- Program grompp, VERSION 4.5.5 Source code file: toppush.c, line: 1987 Fatal error: No such moleculetype NA+ For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Regards Kirubakaran P -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Regarding Extension of the potential lookup tables
On 4/11/2011 10:41 PM, Ravi Kumar Venkatraman wrote: *Dear All, Could anybody tell me what is the purpose of Extension of the potential lookup tables beyond the cut-off.* Check out manual 7.3.12 *I have read somewhere that the sum the smallest diagnol of the box and rlist should be equal to table-extension. Please explain me the same.* I doubt that you read that. Mark *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Gromacs query for vaccum medium
I have seen different articles on MD simulation in vaccum but i didn't get the exact way for it.If u can tell me the exact way then i can proceed for it fastly because I have to do it within certain time limit. On Thu, Nov 3, 2011 at 11:43 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/11/2011 4:58 AM, Anushree Tripathi wrote: Let me know how to simulate a membrane protein in vaccum medium by using gromacs commands.What are the basic differences in commands as well as parameters used in liquid and vaccum medium? Please guide me. I suggest you do all the GROMACS tutorial material you can find, and supplement that with reading several published articles that do simulations with objectives similar to yours. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Thioester bond problem
Dear Gromacs users, I'm attempting to simulate a system composed of two proteins containing a thioester bond between the C-terminus of chain A and a cysteine residue from chain B. I wonder if the parameters for this bond to be included in the .top file exist. Also, I am having troubles figuring out how to include them, since the thioester generates a branch between the two chains. A possible strategy I have come up with is to use specbond.dat in order to create a bond, and then try to add by hand the parameters in the .top file. The problem with this would be to erase an hydroxyl group from the C terminus and a hydrogen atom from the sulfidrilic group. Also, with specbond.dat (even changing cutoffs) the target bond is not the only one that is created by pdb2gmx, since unfortunately another cisteine is closely located to a glicine residue (the same residue I have in C-terminus). I am very grateful for any assistence you could provide. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Steered MD in reverse direction?
Thanks for the suggestion. Also, I was wondering how one can get the time profile of the irreversible work from the gromacs pull-code out put . From constant pulling-rate SMD, we get time profile of force pullf.xvg and pullx.xvg. I wonder does multiplying the the value from pullx.xvg and value from pullf.xvg will provide the work . Or, will it be force ( obtained from pullf.xvg) multiplied by pulling rate multiplied by time ? From: Justin A. Lemkul jalem...@vt.edu To: Sanku M msank...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, November 3, 2011 9:27 PM Subject: Re: [gmx-users] Steered MD in reverse direction? Sanku M wrote: Hi, I am performing steered Molecular dynamics simulation to pull a molecule out of a complex. I am using gromacs 4.5.4 to perform the constant rate pulling..I have done the steered MD simulation in a particular direction i.e hav pulled the molecule out of complex. But, to check the convergence/hysterisis of the pulled path way, I would like to perform the same steered MD in reverse direction i.e push the molecule back into the complex. But, I was wondering, to perform the backward steered MD, how should I modify the .mdp parameters? Should I make the pull_rate1 negative or switch the pull_group0 and pull_group1 ? Any help will be appreciated. Use a negative pull rate. But simple pulling like this can be difficult; you're now trying to hit a moving target. A slight rotation of the protein can render the whole simulation junk - your pulled molecule may smack into some undesired location. -Justin The following is the part of the pull-code parameter I am using: ; Pull code pull = umbrella pull_geometry = distance ; simple distance increase pull_dim = N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups = 1 pull_group0 = Mol_A pull_group1 = Mol_B pull_rate1 = 0.0025 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 Sanku -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] PMF when pulling in -Z direction
Dear Gromacs Users, I am trying to study ligand unbinding adopting Umbrella sampling (using Gmx 4.5.3). during my initial pull to generate configurations for umbrella windows I have pulled in the -Z direction, @ s0 legend 0 Z @ s1 legend 1 dZ 0. 7.37361 -0.33625 0.0200 7.37377 -0.33631 0.0400 7.37404 -0.33637 0.0600 7.3744 -0.33643 0.0800 7.37473 -0.33649 . . . . 321.0800 7.37523 -1.29949 321.1000 7.37442 -1.29955 321.1200 7.37374 -1.29961 321.1400 7.37355 -1.29967 321.1600 7.37404 -1.29973 321.1800 7.37491 -1.29979 321.2000 7.3757 -1.29985 321.2200 7.37608 -1.29991 321.2400 7.37595 -1.29997 321.2600 7.37518 -1.30003 321.2800 7.37395 -1.30009 . . .(so on) Now when I ran simulations in each umbrella windows, the PMF energies are in negative. My guess is that this is due to my initial setup, or is there something seriously wrong. And if i am right I should get the correct PMF by taking the negative of this PMF (or is it)?? - ; Pull code (pulling simulation) pull = constraint pull_geometry = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = Protein pull_group1 = MAL pull_rate1 = 0.005 ; pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout = 500 ; every 1 ps pull_nstfout = 500 ; every 1 ps - ; Pull code (Umbrella simulation) pull = umbrella pull_geometry = distance ; pull_dim = Y Y Y pull_start = yes ; pull_ngroups = 1 pull_group0 = Protein pull_group1 = MAL pull_rate1 = 0.000 ; pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout = 500 ; every 1 ps pull_nstfout = 500 ; every 1 ps Best, nahren-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Gromacs query for vaccum medium
Anushree Tripathi wrote: I have seen different articles on MD simulation in vaccum but i didn't get the exact way for it.If u can tell me the exact way then i can proceed for it fastly because I have to do it within certain time limit. It would be useful if you were to describe what it is that you're trying to replicate, why you don't understand how to do it, and what you have tried. Implying urgency or time limits is not appropriate; we all have things that we're working on and we're all trying to make progress on our own projects (and some of us are nearing completion on dissertations). The contributors to this list take time to offer free advice when they can. They can do so effectively and efficiently with a clear statement of goals and specific questions. -Justin On Thu, Nov 3, 2011 at 11:43 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 4/11/2011 4:58 AM, Anushree Tripathi wrote: Let me know how to simulate a membrane protein in vaccum medium by using gromacs commands.What are the basic differences in commands as well as parameters used in liquid and vaccum medium? Please guide me. I suggest you do all the GROMACS tutorial material you can find, and supplement that with reading several published articles that do simulations with objectives similar to yours. Mark -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Thioester bond problem
alberto arrigoni wrote: Dear Gromacs users, I'm attempting to simulate a system composed of two proteins containing a thioester bond between the C-terminus of chain A and a cysteine residue from chain B. I wonder if the parameters for this bond to be included in the .top file exist. Also, I am having troubles figuring out how to include them, since the thioester generates a branch between the two chains. A possible strategy I have come up with is to use specbond.dat in order to create a bond, and then try to add by hand the parameters in the .top file. The problem with this would be to erase an hydroxyl group from the C terminus and a hydrogen atom from the sulfidrilic group. Also, with specbond.dat (even changing cutoffs) the target bond is not the only one that is created by pdb2gmx, since unfortunately another cisteine is closely located to a glicine residue (the same residue I have in C-terminus). I am very grateful for any assistence you could provide. There are several things I can think of to try. First, have you used the -chainsep ter option in pdb2gmx? It shouldn't create termini based on chain identifiers, but rather on TER entries, which, if removed, don't create problems. You can also use the -ter option to interactively select termini states, thus adding no terminal acid group atoms to the actual C-terminus of the first chain. -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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Regarding Extension of the potential lookup tables beyond the cut-of
*Dear All, Ok, I don't remember the site. But please explain me about the purpose of table extension. Thank you * *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] PMF when pulling in -Z direction
nahren manuel wrote: Dear Gromacs Users, I am trying to study ligand unbinding adopting Umbrella sampling (using Gmx 4.5.3). during my initial pull to generate configurations for umbrella windows I have pulled in the -Z direction, @ s0 legend 0 Z @ s1 legend 1 dZ 0.7.37361-0.33625 0.02007.37377-0.33631 0.04007.37404-0.33637 0.06007.3744-0.33643 0.08007.37473-0.33649 . . . . 321.08007.37523-1.29949 321.10007.37442-1.29955 321.12007.37374-1.29961 321.14007.37355-1.29967 321.16007.37404-1.29973 321.18007.37491-1.29979 321.20007.3757-1.29985 321.22007.37608-1.29991 321.24007.37595-1.29997 321.26007.37518-1.30003 321.28007.37395-1.30009 . . .(so on) Now when I ran simulations in each umbrella windows, the PMF energies are in negative. My guess is that this is due to my initial setup, or is there something seriously wrong. And if i am right I should get the correct PMF by taking the negative of this PMF (or is it)?? So your PMF is negative, why is that a problem? A negative binding energy indicates favorability of binding. -Justin - ; Pull code (pulling simulation) pull= constraint pull_geometry = distance pull_dim= N N Y pull_start = yes pull_ngroups= 1 pull_group0 = Protein pull_group1 = MAL pull_rate1 = 0.005 ; pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout= 500 ; every 1 ps pull_nstfout= 500 ; every 1 ps - ; Pull code (Umbrella simulation) pull= umbrella pull_geometry = distance ; pull_dim= Y Y Y pull_start = yes ; pull_ngroups= 1 pull_group0 = Protein pull_group1 = MAL pull_rate1 = 0.000 ; pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout= 500 ; every 1 ps pull_nstfout= 500 ; every 1 ps Best, nahren -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Thioester bond problem
Hi Alberto, I used a stupid method to deal with this kind of non-standard moiety. You can use AmberTools to parameterize your thioester, together with your proteins, and then use acpype to convert they topology and coordinate files to gromacs format. But I am not sure if you want to use amber force field. Yun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] PMF when pulling in -Z direction
Hi Justin, If you observe my pulling simulation, you will see that the distances are (increasing) in the negative. Here is the PMF (image): http://www.flickr.com/photos/nahrenmascarenhas/6312990056/ this is not one expects in ligand unbinding. (of course these are from my initial simulations, approx. 1 ns runs in 5 windows) Best, nahren From: Justin A. Lemkul jalem...@vt.edu To: nahren manuel meetnah...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, November 4, 2011 7:44 PM Subject: Re: [gmx-users] PMF when pulling in -Z direction nahren manuel wrote: Dear Gromacs Users, I am trying to study ligand unbinding adopting Umbrella sampling (using Gmx 4.5.3). during my initial pull to generate configurations for umbrella windows I have pulled in the -Z direction, @ s0 legend 0 Z @ s1 legend 1 dZ 0. 7.37361 -0.33625 0.0200 7.37377 -0.33631 0.0400 7.37404 -0.33637 0.0600 7.3744 -0.33643 0.0800 7.37473 -0.33649 . . . . 321.0800 7.37523 -1.29949 321.1000 7.37442 -1.29955 321.1200 7.37374 -1.29961 321.1400 7.37355 -1.29967 321.1600 7.37404 -1.29973 321.1800 7.37491 -1.29979 321.2000 7.3757 -1.29985 321.2200 7.37608 -1.29991 321.2400 7.37595 -1.29997 321.2600 7.37518 -1.30003 321.2800 7.37395 -1.30009 . . .(so on) Now when I ran simulations in each umbrella windows, the PMF energies are in negative. My guess is that this is due to my initial setup, or is there something seriously wrong. And if i am right I should get the correct PMF by taking the negative of this PMF (or is it)?? So your PMF is negative, why is that a problem? A negative binding energy indicates favorability of binding. -Justin - ; Pull code (pulling simulation) pull = constraint pull_geometry = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = Protein pull_group1 = MAL pull_rate1 = 0.005 ; pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout = 500 ; every 1 ps pull_nstfout = 500 ; every 1 ps - ; Pull code (Umbrella simulation) pull = umbrella pull_geometry = distance ; pull_dim = Y Y Y pull_start = yes ; pull_ngroups = 1 pull_group0 = Protein pull_group1 = MAL pull_rate1 = 0.000 ; pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout = 500 ; every 1 ps pull_nstfout = 500 ; every 1 ps Best, nahren -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] PMF when pulling in -Z direction
nahren manuel wrote: Hi Justin, If you observe my pulling simulation, you will see that the distances are (increasing) in the negative. Exactly as you expect. You're pulling along the -Z dimension, as you said before. So the ligand is pulled from the protein to an increasingly negative position. Here is the PMF (image): http://www.flickr.com/photos/nahrenmascarenhas/6312990056/ this is not one expects in ligand unbinding. (of course these are from my initial simulations, approx. 1 ns runs in 5 windows) Don't base any conclusions on what you see. The simulation time and number of windows are both woefully insufficient to make any reliable observations. Only once you have done a proper set of umbrella sampling windows will you be able to tell what's going on. You should also be doing error estimates when computing the PMF; I suspect the error bars will be as wild as the values in the PMF plot. -Justin Best, nahren *From:* Justin A. Lemkul jalem...@vt.edu *To:* nahren manuel meetnah...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Friday, November 4, 2011 7:44 PM *Subject:* Re: [gmx-users] PMF when pulling in -Z direction nahren manuel wrote: Dear Gromacs Users, I am trying to study ligand unbinding adopting Umbrella sampling (using Gmx 4.5.3). during my initial pull to generate configurations for umbrella windows I have pulled in the -Z direction, @ s0 legend 0 Z @ s1 legend 1 dZ 0.7.37361-0.33625 0.02007.37377-0.33631 0.04007.37404-0.33637 0.06007.3744-0.33643 0.08007.37473-0.33649 . . . . 321.08007.37523-1.29949 321.10007.37442-1.29955 321.12007.37374-1.29961 321.14007.37355-1.29967 321.16007.37404-1.29973 321.18007.37491-1.29979 321.20007.3757-1.29985 321.22007.37608-1.29991 321.24007.37595-1.29997 321.26007.37518-1.30003 321.28007.37395-1.30009 . . .(so on) Now when I ran simulations in each umbrella windows, the PMF energies are in negative. My guess is that this is due to my initial setup, or is there something seriously wrong. And if i am right I should get the correct PMF by taking the negative of this PMF (or is it)?? So your PMF is negative, why is that a problem? A negative binding energy indicates favorability of binding. -Justin - ; Pull code (pulling simulation) pull= constraint pull_geometry = distancepull_dim= N N Y pull_start = yespull_ngroups= 1 pull_group0= Protein pull_group1= MAL pull_rate1 = 0.005 ; pull_k1= 1000 ; kJ mol^-1 nm^-2 pull_nstxout= 500 ; every 1 ps pull_nstfout= 500 ; every 1 ps - ; Pull code (Umbrella simulation) pull= umbrella pull_geometry = distance ; pull_dim= Y Y Y pull_start = yes ; pull_ngroups= 1 pull_group0= Protein pull_group1= MAL pull_rate1 = 0.000 ; pull_k1= 1000 ; kJ mol^-1 nm^-2 pull_nstxout= 500 ; every 1 ps pull_nstfout= 500 ; every 1 ps Best, nahren -- 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 -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] query for energy minimization in solvent
when i run the given command i.e, grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr It is showing fatal error:No such molecule type NA. How could I troubleshoot this problem? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] query for energy minimization in solvent
Anushree Tripathi wrote: when i run the given command i.e, grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr It is showing fatal error:No such molecule type NA. How could I troubleshoot this problem? Ion naming is listed in ions.itp - the NA name works for all force fields in the Gromacs 4.5.x series. Older versions had force field-specific naming so you will have to change the name accordingly if you're using one of these versions. -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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Regarding Extension of the potential lookup tables beyond the cut-of
Ravi Kumar Venkatraman wrote: *Dear All, Ok, I don't remember the site. But please explain me about the purpose of table extension. Please refer to http://manual.gromacs.org/online/mdp_opt.html#table and the manual, section 6.7.2. -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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Regarding Extension of the potential lookup tables beyond the cut-of
On 5/11/2011 5:35 AM, Ravi Kumar Venkatraman wrote: *Dear All, Ok, I don't remember the site. But please explain me about the purpose of table extension. * Sorry, I have other things to do than refute statements that you can't attribute, when you don't appear to have managed to read the manual reference I gave you last time. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] B-factor to large? Input for TLS
Dear Gromacs Users and Experts, I want to calculate from my xtc trajectory the B-factor and the anisotropic temperature factor. I'm using following gromacs command: $ g_rmsf -f traj.xtc -o rmsf.xvg -oq bfac.pdb -ox bfac2.pdb -s structure.pdb I want to input the resulting PDB file to the TLS Server [1] to calculate the hinge residues for my system. The B-factor which g_rmsf is calculating seem to be to large, they are in the range of 2000 to 6000 (last column without the 1.00 prefix) [2]. The website [3] suggests that a reasonable B-factor should is in the range of 21 to 200. Also the TLS server [1] complains that the b-factors are in the wrong range. I did several test but I have no idea what Im doing wrong. The trajectory is with 250ns long enough to get for my small system a convergence on the B-factor. - I thought it could be a unit problem, what are the B-factor units which g_rmsf uses? Could this cause such an huge difference in the b-factor? - What is the standard unit for the b-factor in the PDB definition (from the PDB database)? - What is a realistic range for the b-factor? - What else could be the error source, what am I doing wrong? Thanks, any help is welcome, Henrey ---1: TLSMD SERVER http://skuld.bmsc.washington.edu/~tlsmd/ ---2: bfac2.pdb : ... ATOM 6146 N GLY 435 97.841 52.072 37.712 1.006712.85 ATOM 6147 HN GLY 435 97.972 52.020 37.437 1.006676.79 ATOM 6148 CA GLY 435 97.953 52.003 37.883 1.006739.30 ATOM 6149 HA1 GLY 435 97.975 51.822 37.563 1.006956.61 ATOM 6150 HA2 GLY 435 97.554 52.041 37.972 1.007042.78 ATOM 6151 C GLY 435 98.601 52.111 38.350 1.006210.20 ATOM 6152 O GLY 435 98.552 51.909 38.905 1.006278.92 ATOM 6153 N ASN 436 99.235 52.437 38.127 1.005772.75 ATOM 6154 HN ASN 436 99.262 52.602 37.668 1.005803.67 ATOM 6155 CA ASN 436 99.904 52.574 38.508 1.005343.12 ATOM 6156 HA ASN 436 99.947 52.400 38.918 1.005671.18 ATOM 6157 CB ASN 436 100.537 52.527 37.948 1.005355.63 ATOM 6158 HB1 ASN 436 100.960 52.556 38.127 1.005098.00 ATOM 6159 HB2 ASN 436 100.553 52.657 37.601 1.005272.78 ATOM 6160 CG ASN 436 100.587 52.258 37.586 1.006031.62 ATOM 6161 OD1 ASN 436 100.582 52.138 37.675 1.006435.18 ATOM 6162 ND2 ASN 436 100.641 52.163 37.176 1.006306.09 ATOM 6163 1HD2 ASN 436 100.689 51.993 36.928 1.006834.63 ATOM 6164 2HD2 ASN 436 100.652 52.264 37.117 1.006062.64 ATOM 6165 C ASN 436 99.947 53.023 38.917 1.004590.56 ATOM 6166 O ASN 436 99.651 53.240 38.597 1.004290.70 ... ---3: B-factor range at 3 Å resolution http://www.p212121.com/2009/04/12/b-factor-range-3-resolution/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] How to calculate work
Hi, I am performing steered MD simulation using gromacs. I was wondering how one can get the time profile of the irreversible work from the gromacs pull-code out put . From constant pulling-rate SMD, we get time profile of force pullf.xvg and pullx.xvg. I wonder does multiplying the the value from pullx.xvg and value from pullf.xvg will provide the work . Or, will it be force ( obtained from pullf.xvg) multiplied by pulling rate multiplied by time ? Sanku-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] How to calculate work
Hi Sanku, I was using the pullf.xvg and multiplying it with pulling rate and time. f*v*dt = W and getting the total work for each SMD simulation. I'm not sure if this is the best/correct way to do it. But from original Jarzynski's article (PRL (2007) 78(14), 2690-2693) this is what I deduced. I asked this question but I think very few users of Gromacs do Jarzynski Equality (JE) to get free energy differences. If anyone can comment on this, it will be useful for the community. PS: If you use AMBER, it gives the work profile as the output. You can use the total work which is printed at the last line of the output and get the exponential average of beta*W. PPS: May be you are aware of this issue, but the JE suffers from the fact that you do the exponential average and the smaller work values determine everything. Regards Sai On Fri, Nov 4, 2011 at 7:46 PM, Sanku M msank...@yahoo.com wrote: Hi, I am performing steered MD simulation using gromacs. I was wondering how one can get the time profile of the irreversible work from the gromacs pull-code out put . From constant pulling-rate SMD, we get time profile of force pullf.xvg and pullx.xvg. I wonder does multiplying the the value from pullx.xvg and value from pullf.xvg will provide the work . Or, will it be force ( obtained from pullf.xvg) multiplied by pulling rate multiplied by time ? Sanku -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
