[gmx-users] where is the script?
Hello: I found that someone mentioned that there is a script from Mark which could be used to convert CGenff format into Gromacs .itp file. I searched the mailist and didn't find it. I am just wondering where can I obtain this script? thank you very much best Albert -- 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] Re: energy-mimisation-problem
On Sun, Nov 25, 2012 at 9:08 PM, SANTU BISWAS santu.biswa...@gmail.com wrote: dear users, When performing a energy minimization of a polypeptide(formed by lysine-5-residues) in vacuum box by using Steepest Descent and also Conjugate Gradient methods in gromacs double precision,i noted that GROMACS never converges to emtol values under about 0.1 kj/mol/nm.I have used the .mdp file which is given below title= cpp = /lib/cpp ;include =-I../top/ define = -DFLEXIBLE ; RUN CONTROL PARAMETERS = integrator = steep ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 1000 rlist= 0.9 rcoulomb = 0.9 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw_switch = 0 rvdw = 0.9 ; Neighbour searching nstlist = 1 ; ENERGY MINIMIZATION OPTIONS = emtol= 0.1 emstep = 0.1 nstcgsteep = 1000 santu -- 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] where is the script?
On 2012-11-26 12:00, Albert wrote: Hello: I found that someone mentioned that there is a script from Mark which could be used to convert CGenff format into Gromacs .itp file. I searched the mailist and didn't find it. I am just wondering where can I obtain this script? thank you very much best Albert It's posted on the website. http://www.gromacs.org/Downloads/User_contributions/Other_software You want this one: charmm2gromacs-pvm.py -- 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] Re: force vs time plot
This should be in the pullf.xvg (time and then the forces). Am 24.11.2012 19:55, schrieb gmx-users-requ...@gromacs.org: Hi to all gromacs users, I am trying to run an umbrella sampling and i am getting the initial conformations by pulling simulations but i want to check the simulation through the force vs time plot to see if my complex did or did not separate, so how can i get this plot? Thank you for your time Paula -- 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] GPU warnings
On Sun, Nov 25, 2012 at 8:47 PM, Thomas Evangelidis teva...@gmail.comwrote: Hi Szilárd, I was able to run code compiled with icc 13 on Fedora 17, but as I don't have Intel Compiler v13 on this machine I can't check it now. Please check if it works for you with gcc 4.7.2 (which is the default) and let me know if you succeed. The performance difference between icc and gcc on your processor should be negligible with GPU runs and at most 5-10% with CPU-only runs. As the issue is quite annoying, I'll try to have a look later, probably after the beta is out. gcc 4.7.2 is not supported by any CUDA version. I suggest that you just fix it by editing the include/host_config.h and changing the version check macro (line 82 AFAIK). I've never had real problems with using new and officially not supported gcc-s, the version check is more of a promise from NVIDIA that we've tested thoroughly internally and we more or less vouch for thins combination. Cheers, -- Szilárd PS: Disclamer: I don't take responsibility if your machine goes up in flames! ;) Thomas -- 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
Re: [gmx-users] Is any command to distinguish gromacs 4.5.4 and 4.5.5
Or run any binary with the -version option e.g: $ mdrun -version -- Szilárd On Sun, Nov 25, 2012 at 10:30 AM, Mark Abraham mark.j.abra...@gmail.comwrote: Look at the top of the output of any GROMACS program. Mark On Sun, Nov 25, 2012 at 10:06 AM, Acoot Brett acootbr...@yahoo.com wrote: Dear All, Is any gromacs command which can tell us or distinguish whether what installed is gromacs 4.5.4 or 4.5.5? Cheers, Acoot --- On Sat, 24/11/12, David van der Spoel sp...@xray.bmc.uu.se wrote: From: David van der Spoel sp...@xray.bmc.uu.se Subject: Re: [gmx-users] Different average H bonds with different g_hbond releases To: Discussion list for GROMACS users gmx-users@gromacs.org Received: Saturday, 24 November, 2012, 5:30 PM On 2012-11-24 05:41, Acoot Brett wrote: If we got the results by 4.5.4, what will be the method to analyze it by 4.5.5? By a pathch or by installation of 4.5.5 to analyze the 4.5.4 results? In practice there is no problem to have a number of gromacs versions installed. It is typically not recommended to switch gromacs versions of mdrun during a project - unless there are know issues - but for the analysis this is less critical. In this case 4.5.5 should be used. Cheers, Acoot --- On Sat, 24/11/12, Justin Lemkul jalem...@vt.edu wrote: From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Different average H bonds with different g_hbond releases To: Discussion list for GROMACS users gmx-users@gromacs.org Received: Saturday, 24 November, 2012, 9:30 AM On 11/23/12 5:23 PM, Luigi CAVALLO wrote: Hi, we have a .xtc and .tpr file. We were interested in the average number of H-bonds in the last 10ns of a 60ns long trajectory. We analyzed the jobs as g_hbond -f traj1_0-60ns.xtc -s topol.tpr -b 5 -num hbond.xvg. We are displaced by having a different number depending on the g_hbond release. Release 4.5.4 : Average number of hbonds per timeframe 163.620 out of 118112 possible Release 4.5.5 : Average number of hbonds per timeframe 168.168 out of 118112 possible Looking at the hbond.xvg file, the number of H-bonds in each frame are clearly different between the two releases. How is this possible ? We checked single versus double precision g_hbonds, same behavior. We checked that the initial part of the output, i.e. all the various g_hbond defaults, they are the same. We tested different computers and compilations, same behavior. The topology and the md run were done with release 4.5.4 if this could be a relevant information. There was a bug that was fixed in May 2011 wherein 4.5.4 reported too few hydrogen bonds. commit 91a481fad7ef0d87a4f8b2cb633c9dc40644350c Author: Erik Marklund er...@anfinsen.bmc.uu.se Date: Tue May 10 14:37:10 2011 +0200 Fixed long standing bug where the merging resulted in too few hbonds. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 -- 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.se http://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 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
Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0
On 11/26/12 12:58 AM, Venkat Reddy wrote: Dear all, I am simulating a Protein-Drug complex. I am following Justin's tutorial. I have used *PRODRG *for generating topology. *Gaussian *has given me the ESP charges. I have edited the charges in the itp file using the *Gaussian*'s ESP charges*. *Then I am getting this strange error. *ERROR 1 [file protein.top, line 75]:* * atom C4 (Res ORP-1) has mass 0* * * * * * * *ERROR 2 [file protein.top, line 75]:* * atom C14 (Res ORP-1) has mass 0* Probably there are some hidden line ending problems. Did you edit the file with a plain text editor? Also note... 24 CH2 1 ORP C5 40.354 13.0190 *25 CH1 1 ORP C4 4 -0.024 14.0270* These masses don't make sense. CH2 should have a mass of 14.027 and CH1 should have a mass of 13.019. I've never seen PRODRG get something like this wrong; were you sure to carefully change the file? It seems something has gone very wrong here. Compare the original topology (from PRODRG) with the one you edited. If grompp succeeds using the PRODRG topology (stop using it after that point), then the error arose due to something you did when editing the file. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Re: energy-mimisation-problem
On 11/26/12 6:01 AM, SANTU BISWAS wrote: On Sun, Nov 25, 2012 at 9:08 PM, SANTU BISWAS santu.biswa...@gmail.com wrote: dear users, When performing a energy minimization of a polypeptide(formed by lysine-5-residues) in vacuum box by using Steepest Descent and also Conjugate Gradient methods in gromacs double precision,i noted that GROMACS never converges to emtol values under about 0.1 kj/mol/nm.I have used the .mdp file which is given below title= cpp = /lib/cpp ;include =-I../top/ define = -DFLEXIBLE ; RUN CONTROL PARAMETERS = integrator = steep ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 1000 rlist= 0.9 rcoulomb = 0.9 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw_switch = 0 rvdw = 0.9 ; Neighbour searching nstlist = 1 ; ENERGY MINIMIZATION OPTIONS = emtol= 0.1 emstep = 0.1 nstcgsteep = 1000 Are you using single or double precision? Single precision steepest descents is unlikely to ever reach such a low emtol. Double precision and more thorough methods (CG and/or L-BFGS) may achieve it, perhaps after several rounds of each. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Umbrella sampling - regd
On 11/26/12 1:03 AM, ramesh cheerla wrote: Dear Gromacs users, I am calculating PMF for the ion permeation through a tunnel, using umbrella sampling. In my system I have some binding sites with ions, I have removed some ions from binding sites before pulling and In pulling simulations have pullaed pulled the adjacent ions to the vacant binding site (tunnel is aligned along Y- axis). for this I have used the following options in .mdp file. ; Pull code pull= umbrella pull_geometry = distance pull_dim= N Y N pull_start = yes pull_ngroups= 1 pull_group0 = REFA pull_rate1 = 0.01 pull_k1 = 3000 ; kJ mol^-1 nm^-2 Here pull_group0 = REFA is the ion at another binding site and pull_group1 = ATBP is the atom that I am pulling to the vacant site. In next step I have performed umbrella sampling simulations to the selected configurations using the following options : ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= N Y N pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = REFA pull_group1 = ATBP pull_init1 = 0 pull_rate1 = 0.0 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 3000 ; kJ mol^-1 nm^-2 pull_nstxout= 100 pull_nstfout= 100 After that I have constructed PMF profile using Gromacs tool g_wham, while using g_wham I am getting the following warnings, WARNING, no data point in bin 34 (z=0.889382) ! You may not get a reasonable profile. Check your histograms! I have checked my histograms instead of one histogram for each configuration with perfect overlapping, I am getting only one histogram. You're probably just plotting the file wrong. xmgrace -nxy histo.xvg Here I am sending the link that containing PMF profile and histogram that have obtained. http://researchweb.iiit.ac.in/~bipin.singh/pmf.jpg http://researchweb.iiit.ac.in/~bipin.singh/hist.jpg The PMF suggests massive undersampling (or complete lack of sampling) in several areas. the weired thing that I have observed in my pulling simulations is that I have expected motion of ion in positive Y-direction for my pull parameters but it is moving in negative Y- direction. Can anybody please suggest me a solution for this, Am I following correct protocol to get PMF of my system, is there any better method that suits for my system. If you are trying to see a complete translocation of an ion through a channel, the distance geometry is inappropriate, as it does not deal correctly with the change of sign for the vector between the reference and pulled group, IIRC. Try position geometry and associated settings. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] where is the script?
On 11/26/2012 02:36 PM, David van der Spoel wrote: It's posted on the website. http://www.gromacs.org/Downloads/User_contributions/Other_software You want this one:charmm2gromacs-pvm.py -- thanks a lot for kind reply. But how to use it? I am trying to run with command: python charmm2gromacs-pvm.py charmm.rtf but it said: Traceback (most recent call last): File charmm2gromacs-pvm.py, line 33, in module parFile = open(sys.argv[2], 'r') IndexError: list index out of range I open the script, it said: inparameters: command line parameters: 1charmm topology file 2corresponding charmm parameter file 3optfoldername, default cgenff.ff outfiles: 1foldername/atomtypes.atp 2foldername/forcefield.itp 3foldername/forcefield.doc 4foldername/aminoacids.rtp 5foldername/ffbonded.itp 6foldername/ffnonbonded.itp 7foldername/forcefield.r2b 8optfoldername/lipids.rtp(if '!lipid section' statement in CHARMM top file) 9optfoldername/cmap.itp(if genCMAP = True) It seems that the input file is a folder instead of a single file? I generate my ligand topology from the CGenFF website and I only get a .rst file THX -- 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] ERROR 1: atom C4 (Res ORP-1) has mass 0
Dear Justin, I haven't touched the *Mass column.* I have edited the charges only using gedit in linux. On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/26/12 12:58 AM, Venkat Reddy wrote: Dear all, I am simulating a Protein-Drug complex. I am following Justin's tutorial. I have used *PRODRG *for generating topology. *Gaussian *has given me the ESP charges. I have edited the charges in the itp file using the *Gaussian*'s ESP charges*. *Then I am getting this strange error. *ERROR 1 [file protein.top, line 75]:* * atom C4 (Res ORP-1) has mass 0* * * * * * * *ERROR 2 [file protein.top, line 75]:* * atom C14 (Res ORP-1) has mass 0* Probably there are some hidden line ending problems. Did you edit the file with a plain text editor? Also note... 24 CH2 1 ORP C5 40.354 13.0190 *25 CH1 1 ORP C4 4 -0.024 14.0270* These masses don't make sense. CH2 should have a mass of 14.027 and CH1 should have a mass of 13.019. I've never seen PRODRG get something like this wrong; were you sure to carefully change the file? It seems something has gone very wrong here. Compare the original topology (from PRODRG) with the one you edited. If grompp succeeds using the PRODRG topology (stop using it after that point), then the error arose due to something you did when editing the file. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] ERROR 1: atom C4 (Res ORP-1) has mass 0
On 11/26/12 9:12 AM, Venkat Reddy wrote: Dear Justin, I haven't touched the *Mass column.* I have edited the charges only using gedit in linux. Regardless, the masses I pointed out are wrong. You should still do the test to #include the original topology and see if it works, then if it does, figure out the source of the error in your file. -Justin On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/26/12 12:58 AM, Venkat Reddy wrote: Dear all, I am simulating a Protein-Drug complex. I am following Justin's tutorial. I have used *PRODRG *for generating topology. *Gaussian *has given me the ESP charges. I have edited the charges in the itp file using the *Gaussian*'s ESP charges*. *Then I am getting this strange error. *ERROR 1 [file protein.top, line 75]:* * atom C4 (Res ORP-1) has mass 0* * * * * * * *ERROR 2 [file protein.top, line 75]:* * atom C14 (Res ORP-1) has mass 0* Probably there are some hidden line ending problems. Did you edit the file with a plain text editor? Also note... 24 CH2 1 ORP C5 40.354 13.0190 *25 CH1 1 ORP C4 4 -0.024 14.0270* These masses don't make sense. CH2 should have a mass of 14.027 and CH1 should have a mass of 13.019. I've never seen PRODRG get something like this wrong; were you sure to carefully change the file? It seems something has gone very wrong here. Compare the original topology (from PRODRG) with the one you edited. If grompp succeeds using the PRODRG topology (stop using it after that point), then the error arose due to something you did when editing the file. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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 -- Justin A. Lemkul, Ph.D. Research Scientist 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] ERROR 1: atom C4 (Res ORP-1) has mass 0
Thanks Justin...I will certainly do. On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/26/12 9:12 AM, Venkat Reddy wrote: Dear Justin, I haven't touched the *Mass column.* I have edited the charges only using gedit in linux. Regardless, the masses I pointed out are wrong. You should still do the test to #include the original topology and see if it works, then if it does, figure out the source of the error in your file. -Justin On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/26/12 12:58 AM, Venkat Reddy wrote: Dear all, I am simulating a Protein-Drug complex. I am following Justin's tutorial. I have used *PRODRG *for generating topology. *Gaussian *has given me the ESP charges. I have edited the charges in the itp file using the *Gaussian*'s ESP charges*. *Then I am getting this strange error. *ERROR 1 [file protein.top, line 75]:* * atom C4 (Res ORP-1) has mass 0* * * * * * * *ERROR 2 [file protein.top, line 75]:* * atom C14 (Res ORP-1) has mass 0* Probably there are some hidden line ending problems. Did you edit the file with a plain text editor? Also note... 24 CH2 1 ORP C5 40.354 13.0190 *25 CH1 1 ORP C4 4 -0.024 14.0270* These masses don't make sense. CH2 should have a mass of 14.027 and CH1 should have a mass of 13.019. I've never seen PRODRG get something like this wrong; were you sure to carefully change the file? It seems something has gone very wrong here. Compare the original topology (from PRODRG) with the one you edited. If grompp succeeds using the PRODRG topology (stop using it after that point), then the error arose due to something you did when editing the file. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://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/Searchh**ttp://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 http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] ERROR 1: atom C4 (Res ORP-1) has mass 0
Dear Justin, One more doubt. I am using Gromos 53A6 ff. Can I use Prodrg to generate topology for my ligand? Because, I guess, prodrg uses Gromos 43A1. Can I mix 53A6 and 43A1? On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/26/12 9:12 AM, Venkat Reddy wrote: Dear Justin, I haven't touched the *Mass column.* I have edited the charges only using gedit in linux. Regardless, the masses I pointed out are wrong. You should still do the test to #include the original topology and see if it works, then if it does, figure out the source of the error in your file. -Justin On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/26/12 12:58 AM, Venkat Reddy wrote: Dear all, I am simulating a Protein-Drug complex. I am following Justin's tutorial. I have used *PRODRG *for generating topology. *Gaussian *has given me the ESP charges. I have edited the charges in the itp file using the *Gaussian*'s ESP charges*. *Then I am getting this strange error. *ERROR 1 [file protein.top, line 75]:* * atom C4 (Res ORP-1) has mass 0* * * * * * * *ERROR 2 [file protein.top, line 75]:* * atom C14 (Res ORP-1) has mass 0* Probably there are some hidden line ending problems. Did you edit the file with a plain text editor? Also note... 24 CH2 1 ORP C5 40.354 13.0190 *25 CH1 1 ORP C4 4 -0.024 14.0270* These masses don't make sense. CH2 should have a mass of 14.027 and CH1 should have a mass of 13.019. I've never seen PRODRG get something like this wrong; were you sure to carefully change the file? It seems something has gone very wrong here. Compare the original topology (from PRODRG) with the one you edited. If grompp succeeds using the PRODRG topology (stop using it after that point), then the error arose due to something you did when editing the file. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://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/Searchh**ttp://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 http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] ERROR 1: atom C4 (Res ORP-1) has mass 0
On 11/26/12 9:35 AM, Venkat Reddy wrote: Dear Justin, One more doubt. I am using Gromos 53A6 ff. Can I use Prodrg to generate topology for my ligand? Because, I guess, prodrg uses Gromos 43A1. Can I mix 53A6 and 43A1? PRODRG doesn't even do a very good job of being compatible with 43A1, so if you re-derive the charges correctly, the result is compatible with 53A6. PRODRG basically just uses 43A1 atom types, the names of which are largely the same in 53A6, even if the parameters are slightly different, and thus I view PRODRG as a method to create generic Gromos96 topologies, given that the user has to do a fair amount of work to create a usable topology anyway. -Justin On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/26/12 9:12 AM, Venkat Reddy wrote: Dear Justin, I haven't touched the *Mass column.* I have edited the charges only using gedit in linux. Regardless, the masses I pointed out are wrong. You should still do the test to #include the original topology and see if it works, then if it does, figure out the source of the error in your file. -Justin On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/26/12 12:58 AM, Venkat Reddy wrote: Dear all, I am simulating a Protein-Drug complex. I am following Justin's tutorial. I have used *PRODRG *for generating topology. *Gaussian *has given me the ESP charges. I have edited the charges in the itp file using the *Gaussian*'s ESP charges*. *Then I am getting this strange error. *ERROR 1 [file protein.top, line 75]:* * atom C4 (Res ORP-1) has mass 0* * * * * * * *ERROR 2 [file protein.top, line 75]:* * atom C14 (Res ORP-1) has mass 0* Probably there are some hidden line ending problems. Did you edit the file with a plain text editor? Also note... 24 CH2 1 ORP C5 40.354 13.0190 *25 CH1 1 ORP C4 4 -0.024 14.0270* These masses don't make sense. CH2 should have a mass of 14.027 and CH1 should have a mass of 13.019. I've never seen PRODRG get something like this wrong; were you sure to carefully change the file? It seems something has gone very wrong here. Compare the original topology (from PRODRG) with the one you edited. If grompp succeeds using the PRODRG topology (stop using it after that point), then the error arose due to something you did when editing the file. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://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/Searchh**ttp://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 http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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 -- Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0
Thank yo Justin for your help...I have generated the same topology using *ATB. *Now, I got the masses correctly (as pointed out by you). So, I'm afraid that is there any bug in PRODRG server? On Mon, Nov 26, 2012 at 8:09 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/26/12 9:35 AM, Venkat Reddy wrote: Dear Justin, One more doubt. I am using Gromos 53A6 ff. Can I use Prodrg to generate topology for my ligand? Because, I guess, prodrg uses Gromos 43A1. Can I mix 53A6 and 43A1? PRODRG doesn't even do a very good job of being compatible with 43A1, so if you re-derive the charges correctly, the result is compatible with 53A6. PRODRG basically just uses 43A1 atom types, the names of which are largely the same in 53A6, even if the parameters are slightly different, and thus I view PRODRG as a method to create generic Gromos96 topologies, given that the user has to do a fair amount of work to create a usable topology anyway. -Justin On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/26/12 9:12 AM, Venkat Reddy wrote: Dear Justin, I haven't touched the *Mass column.* I have edited the charges only using gedit in linux. Regardless, the masses I pointed out are wrong. You should still do the test to #include the original topology and see if it works, then if it does, figure out the source of the error in your file. -Justin On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/26/12 12:58 AM, Venkat Reddy wrote: Dear all, I am simulating a Protein-Drug complex. I am following Justin's tutorial. I have used *PRODRG *for generating topology. *Gaussian *has given me the ESP charges. I have edited the charges in the itp file using the *Gaussian*'s ESP charges*. *Then I am getting this strange error. *ERROR 1 [file protein.top, line 75]:* * atom C4 (Res ORP-1) has mass 0* * * * * * * *ERROR 2 [file protein.top, line 75]:* * atom C14 (Res ORP-1) has mass 0* Probably there are some hidden line ending problems. Did you edit the file with a plain text editor? Also note... 24 CH2 1 ORP C5 40.354 13.0190 *25 CH1 1 ORP C4 4 -0.024 14.0270* These masses don't make sense. CH2 should have a mass of 14.027 and CH1 should have a mass of 13.019. I've never seen PRODRG get something like this wrong; were you sure to carefully change the file? It seems something has gone very wrong here. Compare the original topology (from PRODRG) with the one you edited. If grompp succeeds using the PRODRG topology (stop using it after that point), then the error arose due to something you did when editing the file. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin** http://vt.edu/Pages/Personal/**justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.**biochem.vt.**edu/Pages/**Personal/justin http://www.**bevanlab.biochem.vt.edu/Pages/**Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/**listinfo/gmx-users h**ttp://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/Search**h**ttp://www.gromacs.org/**Support/**http://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://**www.gromacs.org/Support/** Mailing_Lists/Searchhttp://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_Listshttp://www.gromacs.org/Support/Mailing_Lists http://**www.gromacs.org/**Support/**Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/**Support/**Mailing_Listshttp://www.gromacs.org/Support/**Mailing_Lists http:/**/www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin
Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0
On 11/26/12 9:43 AM, Venkat Reddy wrote: Thank yo Justin for your help...I have generated the same topology using *ATB. *Now, I got the masses correctly (as pointed out by you). So, I'm afraid that is there any bug in PRODRG server? I have no idea. I haven't used PRODRG in a very long time. -Justin On Mon, Nov 26, 2012 at 8:09 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/26/12 9:35 AM, Venkat Reddy wrote: Dear Justin, One more doubt. I am using Gromos 53A6 ff. Can I use Prodrg to generate topology for my ligand? Because, I guess, prodrg uses Gromos 43A1. Can I mix 53A6 and 43A1? PRODRG doesn't even do a very good job of being compatible with 43A1, so if you re-derive the charges correctly, the result is compatible with 53A6. PRODRG basically just uses 43A1 atom types, the names of which are largely the same in 53A6, even if the parameters are slightly different, and thus I view PRODRG as a method to create generic Gromos96 topologies, given that the user has to do a fair amount of work to create a usable topology anyway. -Justin On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/26/12 9:12 AM, Venkat Reddy wrote: Dear Justin, I haven't touched the *Mass column.* I have edited the charges only using gedit in linux. Regardless, the masses I pointed out are wrong. You should still do the test to #include the original topology and see if it works, then if it does, figure out the source of the error in your file. -Justin On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/26/12 12:58 AM, Venkat Reddy wrote: Dear all, I am simulating a Protein-Drug complex. I am following Justin's tutorial. I have used *PRODRG *for generating topology. *Gaussian *has given me the ESP charges. I have edited the charges in the itp file using the *Gaussian*'s ESP charges*. *Then I am getting this strange error. *ERROR 1 [file protein.top, line 75]:* * atom C4 (Res ORP-1) has mass 0* * * * * * * *ERROR 2 [file protein.top, line 75]:* * atom C14 (Res ORP-1) has mass 0* Probably there are some hidden line ending problems. Did you edit the file with a plain text editor? Also note... 24 CH2 1 ORP C5 40.354 13.0190 *25 CH1 1 ORP C4 4 -0.024 14.0270* These masses don't make sense. CH2 should have a mass of 14.027 and CH1 should have a mass of 13.019. I've never seen PRODRG get something like this wrong; were you sure to carefully change the file? It seems something has gone very wrong here. Compare the original topology (from PRODRG) with the one you edited. If grompp succeeds using the PRODRG topology (stop using it after that point), then the error arose due to something you did when editing the file. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin** http://vt.edu/Pages/Personal/**justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.**biochem.vt.**edu/Pages/**Personal/justin http://www.**bevanlab.biochem.vt.edu/Pages/**Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/**listinfo/gmx-users h**ttp://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/Search**h**ttp://www.gromacs.org/**Support/**http://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://**www.gromacs.org/Support/** Mailing_Lists/Searchhttp://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_Listshttp://www.gromacs.org/Support/Mailing_Lists http://**www.gromacs.org/**Support/**Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/**Support/**Mailing_Listshttp://www.gromacs.org/Support/**Mailing_Lists http:/**/www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080
[gmx-users] maxwell-boltzmann distribution
Hi dear GROMACS experts I wanna know if GROMACS uses only Maxwell-Boltzmann distribution in statistical mechanics, or it also uses Fermi-Dirac and Bose-Einstein statistics.If it only uses Maxwell-Boltzmann distribution, are the results reliable and correct? I mean can we use this law, which is based on the Kinetic Theory of Gases, for a system containing protein (that is not in gaseous state)? If we can use it, why? Bests -Zahra -- 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] Installation problems with MacOS 10.7.5
Dear Users, I have problems with the installation of GROMACS 4.5.5 on MacOS 10.7.5. GCC version 4.2.1 FFTW is: FFTW-3.3.2. The CMAke command cmake -DGMX_THREAD_MPI=OFF \ -DFFTW3F_INCLUDE_DIR=$FFTWDIR/include \ -DFFTW3F_LIBRARIES=$FFTWDIR/lib \ -DGMX_X11=OFF \ -DCMAKE_INSTALL_PREFIX=$(pwd) \ -DGMX_MPI=OFF \ -DGMX_THREADS=OFF \ -DBUILD_SHARED_LIBS=OFF \ /Users/jaschone/Downloads/gromacs-4.5.5 Where CCDIR is the location of the GCC binary, FFTWDIR is the location of the FFTW stuff. I get the following error mesage: WARNING: Target md requests linking to directory /Users/jaschone/progs/lib. Targets may link only to libraries. CMake is dropping the item. and for the other binaries I get similar messages. Using MAKE results in the follwing error: /Users/jaschone/Downloads/gromacs-4.5.5/src/kernel/gmxdump.c:150:11: warning: expression result unused [-Wunused-value] if (state,tpx.bF) { ^ 1 warning generated. Undefined symbols for architecture x86_64: _fftwf_plan_guru_dft_r2c, referenced from: _fft5d_plan_3d in libmd.a(fft5d.c.o) and then similar errors for other routines. The complete STD.OUT and STD.ERR files for the CMAKE and the MAKE command were saved. Does anyone has an idea for an solution? -- 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] g_select error
hello: I am going to calculate the number of water molecules within 6 A of residue 114 by following command: g_select -f md.xtc -s npt3.pdb -os size.xvg -select resid 114 and rdist 0.6 but it said: WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. selection parser: syntax error selection parser: invalid selection 'resid 114 and rdist 0.6' --- Program g_select, VERSION 4.5.5 Source code file: trajana.c, line: 1310 Input error or input inconsistency: selection(s) could not be parsed For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead) -- 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] Umbrella sampling - regd
Dear Justin, I am very thankful to you for your reply, you are correct, I have plotted the histo.xvg file in wrong manner. After plotting histograms in correct manner I have realized that my sampling is very poor as histograms and there overlapping is restricted to some regions only, no histograms in some areas along reaction co-ordinate. I am not sure whether this lack of sampling is due to inappropriate selection of pulled configurations or inappropriate pull geometry. However I will try as per your suggestion and get back to you. Thank you, Regards, Ramesh. On Mon, Nov 26, 2012 at 7:39 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/26/12 1:03 AM, ramesh cheerla wrote: Dear Gromacs users, I am calculating PMF for the ion permeation through a tunnel, using umbrella sampling. In my system I have some binding sites with ions, I have removed some ions from binding sites before pulling and In pulling simulations have pullaed pulled the adjacent ions to the vacant binding site (tunnel is aligned along Y- axis). for this I have used the following options in .mdp file. ; Pull code pull= umbrella pull_geometry = distance pull_dim= N Y N pull_start = yes pull_ngroups= 1 pull_group0 = REFA pull_rate1 = 0.01 pull_k1 = 3000 ; kJ mol^-1 nm^-2 Here pull_group0 = REFA is the ion at another binding site and pull_group1 = ATBP is the atom that I am pulling to the vacant site. In next step I have performed umbrella sampling simulations to the selected configurations using the following options : ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= N Y N pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = REFA pull_group1 = ATBP pull_init1 = 0 pull_rate1 = 0.0 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 3000 ; kJ mol^-1 nm^-2 pull_nstxout= 100 pull_nstfout= 100 After that I have constructed PMF profile using Gromacs tool g_wham, while using g_wham I am getting the following warnings, WARNING, no data point in bin 34 (z=0.889382) ! You may not get a reasonable profile. Check your histograms! I have checked my histograms instead of one histogram for each configuration with perfect overlapping, I am getting only one histogram. You're probably just plotting the file wrong. xmgrace -nxy histo.xvg Here I am sending the link that containing PMF profile and histogram that have obtained. http://researchweb.iiit.ac.in/**~bipin.singh/pmf.jpghttp://researchweb.iiit.ac.in/~bipin.singh/pmf.jpg http://researchweb.iiit.ac.in/**~bipin.singh/hist.jpghttp://researchweb.iiit.ac.in/~bipin.singh/hist.jpg The PMF suggests massive undersampling (or complete lack of sampling) in several areas. the weired thing that I have observed in my pulling simulations is that I have expected motion of ion in positive Y-direction for my pull parameters but it is moving in negative Y- direction. Can anybody please suggest me a solution for this, Am I following correct protocol to get PMF of my system, is there any better method that suits for my system. If you are trying to see a complete translocation of an ion through a channel, the distance geometry is inappropriate, as it does not deal correctly with the change of sign for the vector between the reference and pulled group, IIRC. Try position geometry and associated settings. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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
Re: [gmx-users] Bonds - force constant for given Beads
the distance distribution should be given by the Boltzmann factor of the potential energy function between the beads, assigning V(r)=0 for the most probable distance in your histogram. that's what you get when you take a molecule in vacuum and for instance you compare the dihedral distribution with the dihedral potential, the distribution is just exp[-U(theta)/RT], except maybe for an additive constant. you should be aware that the distribution may change appreciably depending on the environment, so this approach may be tricky: you may include implicit solvent effects on your bonded parameters and then you would end up with a forcefield that counts twice the solvent effects on the internal structure if you add explicit solvent in your model system. I hope it helps. Andre On Mon, Nov 26, 2012 at 2:06 PM, Steven Neumann s.neuman...@gmail.comwrote: Dear Gmx Users, I am planning to build coarse grained model based on the all atom simulation. I created (using VMD) beads representing 2-4 atoms of my protein chain. I want to extract bonded parameters. The equilibrium lenght for bonds (between specified beads) would be the average over the equilibrium from all atom simulation using g_dist between Centre of Mass of group of atoms belonging to given bead. My question: How can I extract the force constant for the bonds from all atom simulation between those beads? Thank you, Steven -- 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 -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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] Installation problems with MacOS 10.7.5
You need to name libraries with FFTW3F_LIBRARIES, not the library path. That explains the dropped dependency and subsequent problems. Mark On Mon, Nov 26, 2012 at 4:19 PM, Stefan Jasconek stjas...@students.uni-mainz.de wrote: Dear Users, I have problems with the installation of GROMACS 4.5.5 on MacOS 10.7.5. GCC version 4.2.1 FFTW is: FFTW-3.3.2. The CMAke command cmake -DGMX_THREAD_MPI=OFF \ -DFFTW3F_INCLUDE_DIR=$FFTWDIR/**include \ -DFFTW3F_LIBRARIES=$FFTWDIR/**lib \ -DGMX_X11=OFF \ -DCMAKE_INSTALL_PREFIX=$(pwd) \ -DGMX_MPI=OFF \ -DGMX_THREADS=OFF \ -DBUILD_SHARED_LIBS=OFF \ /Users/jaschone/Downloads/**gromacs-4.5.5 Where CCDIR is the location of the GCC binary, FFTWDIR is the location of the FFTW stuff. I get the following error mesage: WARNING: Target md requests linking to directory /Users/jaschone/progs/lib. Targets may link only to libraries. CMake is dropping the item. and for the other binaries I get similar messages. Using MAKE results in the follwing error: /Users/jaschone/Downloads/**gromacs-4.5.5/src/kernel/**gmxdump.c:150:11: warning: expression result unused [-Wunused-value] if (state,tpx.bF) { ^ 1 warning generated. Undefined symbols for architecture x86_64: _fftwf_plan_guru_dft_r2c, referenced from: _fft5d_plan_3d in libmd.a(fft5d.c.o) and then similar errors for other routines. The complete STD.OUT and STD.ERR files for the CMAKE and the MAKE command were saved. Does anyone has an idea for an solution? -- 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] g_select error
hello: I am going to calculate the number of water molecules within 6 A of residue 114 by following command: g_select -f md.xtc -s npt3.pdb -os size.xvg -select resid 114 and rdist 0.6 but it said: WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. selection parser: syntax error selection parser: invalid selection 'resid 114 and rdist 0.6' --- Program g_select, VERSION 4.5.5 Source code file: trajana.c, line: 1310 Input error or input inconsistency: selection(s) could not be parsed For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead) -- 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] Re: Bonds - force constant for given Beads
A good start might be: Phys. Chem. Chem. Phys., 2011, 13, 10437–10448 This paper is about hybrid-models (mixing CG and AA). But they discuss 'boltzmann inversion' and 'force matching', which are both methods to obtain CG-potentials. Since they use small molecules it focusses on nonbonded interactions, but one can probably transfer the methods to bonded interactions. Greetings Thomas Am 26.11.2012 18:45, schrieb gmx-users-requ...@gromacs.org: the distance distribution should be given by the Boltzmann factor of the potential energy function between the beads, assigning V(r)=0 for the most probable distance in your histogram. that's what you get when you take a molecule in vacuum and for instance you compare the dihedral distribution with the dihedral potential, the distribution is just exp[-U(theta)/RT], except maybe for an additive constant. you should be aware that the distribution may change appreciably depending on the environment, so this approach may be tricky: you may include implicit solvent effects on your bonded parameters and then you would end up with a forcefield that counts twice the solvent effects on the internal structure if you add explicit solvent in your model system. I hope it helps. Andre On Mon, Nov 26, 2012 at 2:06 PM, Steven Neumanns.neuman...@gmail.comwrote: Dear Gmx Users, I am planning to build coarse grained model based on the all atom simulation. I created (using VMD) beads representing 2-4 atoms of my protein chain. I want to extract bonded parameters. The equilibrium lenght for bonds (between specified beads) would be the average over the equilibrium from all atom simulation using g_dist between Centre of Mass of group of atoms belonging to given bead. My question: How can I extract the force constant for the bonds from all atom simulation between those beads? Thank you, Steven -- 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 avoid adding ions close to ligand
On 2012-11-26 21:28, Yun Shi wrote: Hi everyone, I am doing conventional MD of a protein-ligand system with a mobile loop as part of the binding site. Presumably, the positive Arg side chain on the mobile loop will eventually move towards the negative carboxylic group on my ligand. But I found the addition of NaCl (0.15 M conc.) had some effect on this movement, since the random addition could put Na+ or Cl- ions between the mobile loop and my ligand. I tried generating a index containing only SOL far not close to my ligand, but apparently genion requires a continuous solvent group. So is there any other way to achieve this? Trying different numbers for -seed option seems inefficient and is dependent on luck. Thanks, Yun Maybe your assumption is wrong? Run a long MD simulation and you will find out. -- 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
Re: [gmx-users] g_select error
On 11/26/12 2:08 PM, Albert wrote: hello: I am going to calculate the number of water molecules within 6 A of residue 114 by following command: g_select -f md.xtc -s npt3.pdb -os size.xvg -select resid 114 and rdist 0.6 but it said: WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. selection parser: syntax error selection parser: invalid selection 'resid 114 and rdist 0.6' --- Program g_select, VERSION 4.5.5 Source code file: trajana.c, line: 1310 Input error or input inconsistency: selection(s) could not be parsed For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- You haven't defined rdist to actually be anything. If you need to be using multi-line selections, you should be providing a selection.dat file to -sf instead of using single-line statements to -select. Something like g_select -select 'resname SOL and name OW within 0.6 of resid 114' should do the trick, but I haven't actually tried that so I'm not 100% sure. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] How to avoid adding ions close to ligand
I did hope the ions will move out eventually. But after my ~70ns of conventional MD (with duplicate MD runs and the protein as a dimer with identical sequence), they were still there in the binding site. So I assume it would be much better to start without any salt ions beside my ligand. Could anyone suggest a way around this? Thanks, Yun On Mon, Nov 26, 2012 at 12:39 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2012-11-26 21:28, Yun Shi wrote: Hi everyone, I am doing conventional MD of a protein-ligand system with a mobile loop as part of the binding site. Presumably, the positive Arg side chain on the mobile loop will eventually move towards the negative carboxylic group on my ligand. But I found the addition of NaCl (0.15 M conc.) had some effect on this movement, since the random addition could put Na+ or Cl- ions between the mobile loop and my ligand. I tried generating a index containing only SOL far not close to my ligand, but apparently genion requires a continuous solvent group. So is there any other way to achieve this? Trying different numbers for -seed option seems inefficient and is dependent on luck. Thanks, Yun Maybe your assumption is wrong? Run a long MD simulation and you will find out. -- 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 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 avoid adding ions close to ligand
There is nothing stopping you from replacing the ion in your binding pocket with the original water and then replacing another water elsewhere with the ion at the oxygen's coordintes, then running genconf to renumber the gro file. On 2012-11-26 06:25:47PM -0800, Yun Shi wrote: I did hope the ions will move out eventually. But after my ~70ns of conventional MD (with duplicate MD runs and the protein as a dimer with identical sequence), they were still there in the binding site. So I assume it would be much better to start without any salt ions beside my ligand. Could anyone suggest a way around this? Thanks, Yun On Mon, Nov 26, 2012 at 12:39 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2012-11-26 21:28, Yun Shi wrote: Hi everyone, I am doing conventional MD of a protein-ligand system with a mobile loop as part of the binding site. Presumably, the positive Arg side chain on the mobile loop will eventually move towards the negative carboxylic group on my ligand. But I found the addition of NaCl (0.15 M conc.) had some effect on this movement, since the random addition could put Na+ or Cl- ions between the mobile loop and my ligand. I tried generating a index containing only SOL far not close to my ligand, but apparently genion requires a continuous solvent group. So is there any other way to achieve this? Trying different numbers for -seed option seems inefficient and is dependent on luck. Thanks, Yun Maybe your assumption is wrong? Run a long MD simulation and you will find out. -- 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 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
[gmx-users] itp atomtypes section
Dear users, I apologise if this is a stupid question, however after a morning of searching I have not been able to find the answer. 1. I have a sample itp file and it contains a section like this: [ atomtypes ] CF CF 6 12.011000.2588 A3.5e-01 2.56134e-01 HF HF 1 1.008000.1000 A3.5e-01 4.28529e-01 I can't work out what the column containing the 6 and 1 is for. Can anyone help? It's not documented anywhere that I can find. 2. I notice that there are many types of atomtypes fields. From the manual: [ atomtypes ] ;name mass charge ptype c6 c12 O 15.99940 0.000 A 0.22617E-02 0.74158E-06 OM 15.99940 0.000 A 0.22617E-02 0.74158E-06 This is clearly a different format to my sample above. Why does the format vary? I know the above format is not wrong because it runs succcessfully in a test-run. How does gromacs know which format to use correctly? I appreciate any help. Thank you. Best regards, James -- 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] Validation of topology ....
Dear Gromacs friends, I want to simulate a system containing the biotin. I get the topology from ATB. I want to validate these toplogy for my use . So please could some one told me the way how I can do it ?? I never had any such experience. Is these is any tutorial regarding to these. These is most difficult but needed things in MD. With best wishes and regards, Rama David. -- 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