Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 181, Issue 14
946 3947 3948 3949 3950 3951 3952 3953 3954 3955 3956 > 3973 3974 3975 3976 3977 3978 3979 3980 4117 4118 4119 4120 4121 4122 4123 > 4124 4189 4190 4191 4192 4193 4194 4195 4196 4205 4206 4207 4208 4209 4210 > 4211 4212 4245 4246 4247 4248 4249 4250 4251 4252 4333 4334 4335 4336 4337 > 4338 4339 4340 4381 4382 4383 4384 4385 4386 4387 4388 4637 4638 4639 4640 > 4641 4642 4643 4644 4669 4670 4671 4672 4673 4674 4675 4676 4701 4702 4703 > 4704 4705 4706 4707 4708 4733 4734 4735 4736 4737 4738 4739 4740 4781 4782 > 4783 4784 4785 4786 4787 4788 4861 4862 4863 4864 4865 4866 4867 4868 4893 > 4894 4895 4896 4897 4898 4899 4900 4933 4934 4935 4936 4937 4938 4939 4940 > 5021 5022 5023 5024 5025 5026 5027 5028 5085 5086 5087 5088 5089 5090 5091 > 5092 5117 5118 5119 5120 5121 5122 5123 5124 5189 5190 5191 5192 5193 5194 > 5195 5196 5245 5246 5247 5248 5249 5250 5251 5252 5253 5254 5255 5256 5257 > 5258 5259 5260 5309 5310 5311 5312 5313 5314 5315 5316 5349 5350 5351 5352 > 5353 5354 5355 5356 5373 5374 5375 5376 5377 5378 5379 5380 5453 5454 5455 > 5456 5457 5458 5459 5460 5549 5550 5551 5552 5553 5554 5556 5565 5566 > 5567 5568 5569 5570 5571 5572 5581 5582 5583 5584 5585 5586 5587 5588 5669 > 5670 5671 5672 5673 5674 5675 5676 5693 5694 5695 5696 5697 5698 5699 5700 > 5813 5814 5815 5816 5817 5818 5819 5820 5901 5902 5903 5904 5905 5906 5907 > 5908 5949 5950 5951 5952 5953 5954 5955 5956 5973 5974 5975 5976 5977 5978 > 5979 5980 6005 6006 6007 6008 6009 6010 6011 6012 6061 6062 6063 6064 6065 > 6066 6067 6068 6253 6254 6255 6256 6257 6258 6259 6260 6301 6302 6303 6304 > 6305 6306 6307 6308 6333 6334 6335 6336 6337 6338 6339 6340 6373 6374 6375 > 6376 6377 6378 6379 6380 6389 6390 6391 6392 6393 6394 6395 6396 6413 6414 > 6415 6416 6417 6418 6419 6420 6485 6486 6487 6488 6489 6490 6491 6492 6517 > 6518 6519 6520 6521 6522 6523 6524 6549 6550 6551 6552 6553 6554 6555 6556 > 6573 6574 6575 6576 6577 6578 6579 6580 6629 6630 6631 6632 6633 6634 6635 > 6636 6717 6718 6719 6720 6721 6722 6723 6724 6741 6742 6743 6744 6745 6746 > 6747 6748 > > -- > Ishrat Jahan > Research Scholar > Department Of Chemistry > A.M.U Aligarh > > > -- > > Message: 2 > Date: Tue, 07 May 2019 12:30:50 +0530 > From: sp...@iacs.res.in > To: gmx-us...@gromacs.org > Subject: [gmx-users] water mediated Hbond > Message-ID: > <20190507123050.horde.l85d--hyr0osokdogen6...@mailweb.iacs.res.in> > Content-Type: text/plain; charset=utf-8; format=flowed; DelSp=Yes > > Dear all > I want to determine the water mediated hydrogen between DNA bases and > small molecule. What extra flag should I use in gmx hbond command? Is > there any other option to capture the water mediated Hbonds? Please > suggest something. > Sunipa Sarkar > > > -- > > Message: 3 > Date: Tue, 7 May 2019 09:14:42 +0200 > From: Mark Abraham > To: Discussion list for GROMACS users > Cc: Discussion list for GROMACS users > > Subject: Re: [gmx-users] GROMOS 54A8 Force field > Message-ID: > vd6w5wecjfejgvxm...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi, > > I would contact the authors and ask them. > > Mark > Dear Mark, Thank you very much for your suggestion. Sincerely yours, Kalyanashis Jana > > On Mon, 6 May 2019 at 11:30, Kalyanashis Jana > wrote: > > > Dear users, > > Could you please suggest me where I can get the complete package of > GROMOS > > 54A8 force filed developed by Prof. Dr. Chris Oostenbrink and co-worker ( > > https://pubs.acs.org/doi/10.1021/ct300156h). > > > > Looking forward to your suggestions. > > > > Thanks in advance. > > > > Sincerely yours, > > Kalyanashis Jana > > -- > > 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. > > > > > -- > > Message: 4 > Date: Tue, 7 May 2019 09:14:42 +0200 > From: Mark Abraham > To: Discussion list for GROMACS users > Cc: Discussion list for GROMACS users > > Subject: Re: [gmx-users] GROMOS 54A8 Force field > Message-ID: > vd6w5wecjfejgvxm...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi, > > I would contact the authors and ask them. > > Mark > &
[gmx-users] GROMOS 54A8 Force field
Dear users, Could you please suggest me where I can get the complete package of GROMOS 54A8 force filed developed by Prof. Dr. Chris Oostenbrink and co-worker ( https://pubs.acs.org/doi/10.1021/ct300156h). Looking forward to your suggestions. Thanks in advance. Sincerely yours, Kalyanashis Jana -- 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] REMD analysis
Dear all, I have performed an REMD simulation for protein drug system (8350 + 32500 sol) using gromacs-4.4.5 package. But I could not understand how to do analysis of REMD. I have used 10 set of replicas (298 K to 308.31K with r=1.0038, the common ratio of the geometric progression) for REMD simulation and carried out a 5 ns simulation. I would like to compare the thermodynamics of two drug molecules using REMD. Can you please suggest me, how can I plot potential energy vs probability or how can I get free energy profile? What types of analysis do I need to understand REMD? Looking forward to hear from you. Thanks in advance, Kalyanashis Jana -- 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] Temperature interval in REMD simulations
Dear gromacs user, I am trying to do REMD simulation for protein having 8320 atoms (including protons). The total protein-drug system is solvated with 34269 TIP4P water molecules. I have checked for the temperatures (298.00 to 340.00 K) and no of replicas at "http://folding.bmc.uu.se/remd/; with an exchange probability 0.3. It has suggested 56 replicas and temperatures with r=1.0023, the common ratio of the geometric progression. However, it will be computationally too costly to perform REMD of such a big system with 56 replicas. Could you please suggest me, what temperature limit and exchange probability is enough to produce reasonable results? Thanks in advance, Kalyanashis Jana On Thu, Nov 17, 2016 at 6:11 PM, Kalyanashis Jana <kalyan.chem...@gmail.com> wrote: > Dear gromacs user, > I am trying to do REMD simulation for protein having 8320 atoms (including > protons). The total protein-drug system is solvated with 34269 TIP4P > water molecules. I have checked for the temperatures (298.00 to 340.00 K) > and no of replicas at "http://folding.bmc.uu.se/remd/; with an exchange > probability 0.3. It has suggested 56 replicas and temperatures with > r=1.0023, the common ratio of the geometric progression. However, it will > be computationally too costly to perform REMD of such a big system with 56 > replicas. > > > Could you please suggest me, what temperature limit and exchange > probability is enough to produce reasonable results? > > Thanks with advance, > Kalyanashis Jana > > > > > > > On Fri, Aug 19, 2016 at 5:40 PM, Florent Hédin <w...@fhedin.com> wrote: > >> Dear Ishrat, and dear other gmx-users >> >> I once used the following website, which can help you generating a >> temperature set for REMD simulations >> >> http://folding.bmc.uu.se/remd/ >> >> It is may be the tool you already used for generating you 18 >> temperatures, by the way. By trying different values for the 'exchange >> probability' field you can change the number of temperatures. >> >> It depends on the system size and the number of water molecules of >> course, but try with a larger exchange probability, 0.3 0.4 or 0.5 >> should increase your number of replica. >> >> Regards, >> >> Florent Hédin >> >> On 19/08/16 12:12, asaffa...@post.tau.ac.il wrote: >> > Dear Ishrat, >> > >> > Roughly speaking, the temperatures should be chosen so the acceptance >> > rates between replicas in adjacent temperatures are kept relatively >> > constant. The high temperature should be such that k_B*T_high should be >> > similar to the energy barriers relative to the "equilibrium state". From >> > T_high and up your results should not change. >> > >> > You can take a look at the last paragraph in the appendix of >> > http://www.sciencedirect.com/science/article/pii/S0378437113006468 >> > >> > In addition there is also Hamiltonian REMD (H-REMD) in which the >> > temperature is kept constant and lambda is used instead (not having to >> > worry about the speed of the atoms at high temperatures). >> > >> > See for example >> > https://arxiv.org/pdf/1310.2112v17.pdf, Sec. VI >> > >> > There are references in both links. >> > >> > Best, >> > Asaf >> > >> > Quoting ISHRAT JAHAN <jishra...@gmail.com>: >> > >> >> Dear all >> >> >> >> I am trying to perform REMD simulation of small peptide. I am doing >> REMD >> >> first time. I am not sure how to decide the temperature interval in a >> >> given >> >> range. I have used temperature generator for REMD-simulations for 290 >> >> K to >> >> 500 K with exchange probability of 0.25. It gives 18 replicas. >> However I >> >> am repeating the work done by Zachary et al. I am giving the link here. >> >> http://www.ncbi.nlm.nih.gov/pubmed/25691742 >> >> >> >> >> >> There are 62 replicas generated with temperature range of 290 to 500 K. >> >> >> >> Can anyone tell me how to generate 62 replica with temperature range >> >> of 290 >> >> to 500 K and also tell how to decide the temperature interval for doing >> >> REMD. >> >> How temperature is related to the number of replicas. >> >> >> >> >> >> >> >> Thanks in Advance >> >> -- >> >> Gromacs Users mailing list >> >> >> >> * Please search the archive at >> >> http://www.gromacs.org/Su
Re: [gmx-users] Replica Exchange MD
Thank you very much for your reply and suggestions. I am discussing with system admin regarding this issue. With Best Regards, Kalyanashis Jana On Wed, Oct 5, 2016 at 6:01 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > On Wed, Oct 5, 2016 at 2:17 PM Kalyanashis Jana <kalyan.chem...@gmail.com> > wrote: > > > Hi Mark, > > The MD run stopped after 52.9 ps and the error is > > "MPI: STDOUT or STDERR buffer exhausted. > > MPI: Set MPI_UNBUFFERED_STDIO or output no more than about 8192 > characters > > MPI: between newlines > > > Your MPI library makes assumptions about the MPI application that are > inappropriate. mdrun expects to be able to write to stdout and it works > like stdout. > > Either set the MPI_UNBUFFERED_STDIO variable like it suggests (please talk > to your sysadmins and/or documentation for how to do this, I have no idea, > and little interest in SGI's MPI implementation that causes me as many > problems as all the other implementations put together :-)), or use any > other MPI library you have available. > > Mark > > > > /opt/sgi/mpt/mpt-2.01/bin/mpiexec_mpt: line 52: 29708 Killed > >$mpicmdline_prefix -f $paramfile" > > > > > > I have pasted the equil.mdp, more less similar to the REMD tutorial, for > > your kind perusal. > > > > > > include = > > define = > > integrator = md > > tinit= 0 > > dt = 0.001 > > nsteps = 50 > > init-step= 0 > > simulation-part = 1 > > comm-mode= Linear > > nstcomm = 100 > > comm-grps= > > bd-fric = 0 > > ld-seed = 1993 > > emtol= 10 > > emstep = 0.01 > > niter= 20 > > fcstep = 0 > > nstcgsteep = 1000 > > nbfgscorr= 10 > > rtpi = 0.05 > > nstxout = 250 > > nstvout = 1000 > > nstfout = 0 > > nstlog = 100 > > nstcalcenergy= 100 > > nstenergy= 1000 > > nstxtcout= 0 > > xtc-precision= 1000 > > xtc-grps = > > energygrps = > > ;cutoff-scheme= Verlet > > nstlist = 10 > > ns-type = Grid > > pbc = xyz > > periodic-molecules = no > > ;verlet-buffer-drift = 0.005 > > rlist= 1 > > rlistlong= -1 > > ;nstcalclr= -1 > > coulombtype = PME > > ;coulomb-modifier = Potential-shift-Verlet > > rcoulomb-switch = 0 > > rcoulomb = 1 > > epsilon-r= 1 > > epsilon-rf = 0 > > vdw-type = Cut-off > > ;vdw-modifier = Potential-shift-Verlet > > rvdw-switch = 0 > > rvdw = 1 > > DispCorr = No > > table-extension = 1 > > energygrp-table = > > fourierspacing = 0.12 > > fourier-nx = 0 > > fourier-ny = 0 > > fourier-nz = 0 > > pme-order= 6 > > ewald-rtol = 1e-05 > > ewald-geometry = 3d > > epsilon-surface = 0 > > optimize-fft = yes > > implicit-solvent = No > > gb-algorithm = Still > > nstgbradii = 1 > > rgbradii = 1 > > gb-epsilon-solvent = 80 > > gb-saltconc = 0 > > gb-obc-alpha = 1 > > gb-obc-beta = 0.8 > > gb-obc-gamma = 4.85 > > gb-dielectric-offset = 0.009 > > sa-algorithm = Ace-approximation > > sa-surface-tension = -1 > > tcoupl = v-rescale > > nsttcouple = -1 > > nh-chain-length = 10 > > ;print-nose-hoover-chain-variables = no > > tc-grps = system > > tau-t= 0.1 > > ref-t= 280.00 > > pcoupl = No > > pcoupltype = Isotropic > > nstpcouple = -1 > > tau-p= 1 > > compressibility = > > ref-p= &g
Re: [gmx-users] Replica Exchange MD
= vdw-lambdas = bonded-lambdas = restraint-lambdas= temperature-lambdas = ;calc-lambda-neighbors= 1 init-lambda-weights = ;dhdl-print-energy= no sc-alpha = 0 sc-power = 1 ;sc-r-power = 6 sc-sigma = 0.3 ;sc-coul = no separate-dhdl-file = yes dhdl-derivatives = yes dh_hist_size = 0 dh_hist_spacing = 0.1 acc-grps = accelerate = freezegrps = freezedim= cos-acceleration = 0 deform = ;simulated-tempering = no ;simulated-tempering-scaling = geometric ;sim-temp-low = 300 ;sim-temp-high= 300 E-x = E-xt = E-y = E-yt = E-z = E-zt = ;adress = no user1-grps = user2-grps = userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1= 0 userreal2= 0 userreal3= 0 userreal4= 0 With Best Regards, Kalyanashis Jana On Wed, Oct 5, 2016 at 4:18 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > "It has been abnormally terminated" is too vague to lead to effective help. > What did the terminal and log files say about what led to termination? > > Mark > > On Wed, Oct 5, 2016 at 12:43 PM Kalyanashis Jana <kalyan.chem...@gmail.com > > > wrote: > > > Dear Sotirios, > > Thank you very much for your reply. I have used ΔΤ=10 K, 5K and 3K... > But > > it has been abnormally terminated. > > Is there any possible solution? Please help me... > > Thanks in advance, > > Kalyanashis > > > > On Wed, Oct 5, 2016 at 12:02 PM, Sotirios Dionysios I. Papadatos < > > si.papada...@edu.cut.ac.cy> wrote: > > > > > In this case maybe, just maybe there is a big gap between temperatures. > > > Hence the ΔΕ is to large and the exchange destabilizes your system. > Try a > > > dummy run with a small ΔΤ to see if this is the case > > > > > > ____ > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of > > > Kalyanashis Jana <kalyan.chem...@gmail.com> > > > Sent: Tuesday, October 4, 2016 9:40:08 PM > > > To: Discussion list for GROMACS users > > > Subject: [gmx-users] Replica Exchange MD > > > > > > Dear all, > > > I am trying to perform a REMD simulation for a protein drug complex. I > > have > > > followed REMD tutorial ( > > > http://www.gromacs.org/Documentation/Tutorials/ > GROMACS_USA_Workshop_and_ > > > Conference_2013/An_introduction_to_replica_ > exchange_simulations%3A_Mark_ > > > Abraham,_Session_1B > > > ). > > > I have prepared 10 set for the REMD simulation and generated the tpr > file > > > for MD run. I have used "mpirun -np 10 mdrun_mpi -v -multidir > > > equil[0123456789 <0123-45%2067%2089>]" for MD run. It has been > > abnormally terminated at the > > > middle of the MD run. However, the same topol.tpr files have produced > > > normally terminated MD run when the simulations have been run > > > individually using > > > "mpirun -np 10 mdrun_mpi -v -s topol.tpr " > > > Please suggest me, how can I overcome this problem. > > > Looking forward to hear from you. > > > > > > > > > Thanks in advance, > > > Kalyanashis Jana > > > > > > > > > -- > > > Thanks with regards > > > Kalyanashis Jana > > > -- > > > 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 > > > > >
[gmx-users] Replica Exchange MD
Dear all, I am trying to perform a REMD simulation for a protein drug complex. I have followed REMD tutorial ( http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham,_Session_1B ). I have prepared 10 set for the REMD simulation and generated the tpr file for MD run. I have used "mpirun -np 10 mdrun_mpi -v -multidir equil[0123456789]" for MD run. It has been abnormally terminated at the middle of the MD run. However, the same topol.tpr files have produced normally terminated MD run when the simulations have been run individually using "mpirun -np 10 mdrun_mpi -v -s topol.tpr " Please suggest me, how can I overcome this problem. Looking forward to hear from you. Thanks in advance, Kalyanashis Jana -- Thanks with regards Kalyanashis Jana -- 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] genbox command in gromacs-5.0.1
Dear all, I have installed gromacs-5.0.1 version successfully but when I have run the genbox command, it has shown that This tool has been removed from Gromacs 5.0. Please see http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 for ideas how to perform the same tasks with the new tools. In gromacs site, it is written that genbox This tool has been split to gmx solvate and gmx insert-molecules. Can anyone please help me? Thanks in advance, Kalyanashis Jana -- Kalyanashis Jana email: kalyan.chem...@gmail.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.
[gmx-users] MD run failed..
Dear all, I am doing an MD simulation of a protein system. Energy minimization step has been completed smoothly but the position restraint MD run is not running properly(after 500-900 steps have been stopped automatically). Even it has not shown any error or anything. I have used a drug molecule in the cavity of the active site. When the box size was 10 X 12 X 25, it was run only 100 steps and with 15 X 15 X 28 box size it was run 500-900 steps. I could not understand what is the problem. Can anyone please help me? The pr.mdp file is cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.001 ; ps ! nsteps = 100 ; total 1000.0 ps. nstcomm = 100 nstxout = 250 ; ouput coordinates every 0.5 ps nstvout = 1000 ; output velocities every 2.0 ps nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 100 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes ; V-rescale temparature coupling is on Tcoupl= V-rescale tau_t = 1.01.0-0.1 1.0 1.0 tc_grps = SOLNA protein DRG CL ref_t = 300300300 300 300 ; Pressure coupling is on pcoupl = berendsen ; Use Parrinello-Rahman for research work pcoupltype = isotropic ; Use semiisotropic when working with membranes tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord-scaling= all ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 Thanks in advance, Kalyanashis Jana. -- Kalyanashis Jana email: kalyan.chem...@gmail.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.
[gmx-users] Energy minimization of an UNKNOWN molecule.
Dear all, I am trying to run a gromacs simulation using an .itp file of an unknown molecule ( non protein and DNA). I don't want to put the .itp file in a forcefield folder and I would like put it in my working directory. Can you please tell me, what is procedure to finish the energy minimization? Please help me.. Thanks in advance, Kalyanashis -- Kalyanashis Jana email: kalyan.chem...@gmail.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 of an UNKNOWN molecule.
Thank you so much... I have tried to run the grompp step according to you. But it is showing Fatal error: Syntax error - File A-T.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes I have attached the .itp file and .top file. Please kindly tell me, what to do now.. On Sun, Nov 2, 2014 at 9:15 PM, Victor Rosas Garcia rosas.vic...@gmail.com wrote: just put the itp file in your working directory, and include it in the top file of your system, so that Gromacs can find it. Hope this helps. Victor 2014-11-02 8:54 GMT-06:00 Kalyanashis Jana kalyan.chem...@gmail.com: Dear all, I am trying to run a gromacs simulation using an .itp file of an unknown molecule ( non protein and DNA). I don't want to put the .itp file in a forcefield folder and I would like put it in my working directory. Can you please tell me, what is procedure to finish the energy minimization? Please help me.. Thanks in advance, Kalyanashis -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Kalyanashis Jana email: kalyan.chem...@gmail.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 of an UNKNOWN molecule.
Thank you very much... But I am not going to use any parent molecules like protein or DNA. I would like to perform the gromacs simulation for this unknown molecule. First few lines of my topology file.. ; ; File 'topol.top' was generated ; By user: kollan (506) ; On host: master.localdomain ; At date: Sun Nov 2 20:28:10 2014 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.6.3 ; ; Command line was: ; pdb2gmx -f A-T.pdb -o A-T1.pdb -p topol.top ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters # include A-T.itp ; ; Built itp for A-T.mol2 ;by user vzoete Mon Oct 27 06:32:46 CET 2014 ; ; [ atomtypes ] The yellow colored lines are first seven line A-T.itp file And the error was Fatal error: Syntax error - File A-T.itp, line 7 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes Please help me.. On Mon, Nov 3, 2014 at 1:28 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/14 11:32 AM, Kalyanashis Jana wrote: Thank you so much... I have tried to run the grompp step according to you. But it is showing Fatal error: Syntax error - File A-T.itp, line 7 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes I have attached the .itp file and .top file. Please kindly tell me, what to do now.. Force-field level directives must be declared before molecule-level directives. So if your ligand requires new bonded or nonbonded parameters, or new atom types, it must be #included before the declaration of any [moleculetype]. So put your #include statement for the ligand topology immediately after the #include statement for the parent force field. -Justin On Sun, Nov 2, 2014 at 9:15 PM, Victor Rosas Garcia rosas.vic...@gmail.com wrote: just put the itp file in your working directory, and include it in the top file of your system, so that Gromacs can find it. Hope this helps. Victor 2014-11-02 8:54 GMT-06:00 Kalyanashis Jana kalyan.chem...@gmail.com: Dear all, I am trying to run a gromacs simulation using an .itp file of an unknown molecule ( non protein and DNA). I don't want to put the .itp file in a forcefield folder and I would like put it in my working directory. Can you please tell me, what is procedure to finish the energy minimization? Please help me.. Thanks in advance, Kalyanashis -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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. -- Kalyanashis Jana email: kalyan.chem...@gmail.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.
