[gmx-users] how to convert CGenFF into .itp file?
hello: I found the script charmm2gromacs-pvm.py http://www.gromacs.org/@api/deki/files/185/=charmm2gromacs-pvm.py which claimed could convert the output from CGenFF into Gromacs format. However, I tried many times and it always failed even with the advices from previous thread. This script is trying to generate something like what we see in a complete forcefiled folder instead of a single .itp file for ligand. I am just wondering, how can we convert the output from CGenFF into a single .itp file which is similar to the one from Swissparam? 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
Re: [gmx-users] how to convert CGenFF into .itp file?
You don't. CGenFF is a forcefield, like CHARMM36. You install it, add rtp entries then use pdb2gmx to generate a ligand's topology .itp file On 2012-12-26 11:35:46AM +0100, Albert wrote: hello: I found the script charmm2gromacs-pvm.py http://www.gromacs.org/@api/deki/files/185/=charmm2gromacs-pvm.py which claimed could convert the output from CGenFF into Gromacs format. However, I tried many times and it always failed even with the advices from previous thread. This script is trying to generate something like what we see in a complete forcefiled folder instead of a single .itp file for ligand. I am just wondering, how can we convert the output from CGenFF into a single .itp file which is similar to the one from Swissparam? 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 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 convert CGenFF into .itp file?
On 12/26/2012 12:18 PM, Peter C. Lai wrote: You don't. CGenFF is a forcefield, like CHARMM36. You install it, add rtp entries then use pdb2gmx to generate a ligand's topology .itp file THX but the problem is how to use this script? I've already download the latest CGenFF file from CHARMM FF websiteIt is a folder. -- 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] merge .gro, .top files
Hi KT, To update the number of atoms in a merged .gro file, assuming a single frame and no empty lines after the box definition, you have to replace the second line with the number of lines minus three: sed '2s/^.*$/'$(wc -l file.gro)'/' file.gro out.gro Cheers, Tsjerk On Tue, Dec 25, 2012 at 7:33 AM, Kieu Thu Nguyen kieuthu2...@gmail.comwrote: But i don't see file gromacs_topology_merger.py in the web Vedat gave me. Tsjerk, can you give me the script for updating the number of atoms ? I searched in google, but i have not found it yet. It's really my stupid question, but i don't know why. Thanks ! Best regards, KT On Tue, Dec 18, 2012 at 6:43 PM, Kieu Thu Nguyen kieuthu2...@gmail.com wrote: thank all so much :-) KT On Tue, Dec 18, 2012 at 4:12 PM, Vedat Durmaz dur...@zib.de wrote: there's also an executable topology merger available written in python called gromacs_topology_merger.py as part of a the software package ZIBMolPy designed for conformational analysis at https://github.com/CMD-at-ZIB/**ZIBMolPy https://github.com/CMD-at-ZIB/ZIBMolPy given (in the same directory) a topology file topol.top (argument 1) and two (or more) itp files mol1.itp and mol2.itp included in the top file, the tool writes out a new topology file (argument 2) merging the first two molecules from the include sequence of which itp files are given. note: the number of molecules to be merged should be 1 in the [ molecules ] section. if one of them is meant to appear multiple times in the merged topology, the process needs to be repeated accordingly. vedat Am 18.12.2012 09:38, schrieb Erik Marklund: 18 dec 2012 kl. 09.30 skrev Tsjerk Wassenaar: Hi KT, If you mean concatenating frames in .gro files, you can use trjcat or just cat. If you mean merging the coordinates, it's a wee bit more complicated. Since you also ask for top files, I guess that's the case. Here's a snippet of python code that will do the trick: #!/usr/bin/env python import sys f = [open(i).readlines() for i in sys.argv[1:]] print Merged gro file\n%5d % (sum([len(i) for i in f]) - 3*len(f)) print .join([.join(i[2:-1]) for i in f]), print f[0][-1] For the top files, it is necessary to ensure all the moleculetypes are #included, and that the [ molecules ] listing under [ system ] has the right number and order of the molecules in the merged gro file. There's no tool for that that I know of. In principle you could use grompp for checking that. It would print out a heap of warinngs/notes/errors if structure file and topology don't match. Erik Cheers, Tsjerk On Tue, Dec 18, 2012 at 6:18 AM, Kieu Thu Nguyen kieuthu2...@gmail.com wrote: Dear All, I don't know which tools used to merge 2 files .gro, 2 files .top ? Can i use trjcat ? Thanks ! KT -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/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_Lists http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/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_Lists http://www.gromacs.org/Support/Mailing_Lists --**- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/**elflab/index.html http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to
Re: [gmx-users] how to convert CGenFF into .itp file?
On 12/26/2012 12:39 PM, Peter C. Lai wrote: It should come with two files. A .prm file, which contains the actual forcefield parameters that you use the script to convert to bonded and nonbonded .itp and atomtypes.atp The .rtf file is the charmm equivalent of our .rtp file: it contains some premade residue topologies with charge and connectivity information. I don't know if there are scripts to convert this or not, but it's easy enough to get what you need by hand especially since if your ligand isn't in there, you'll have to create the .rtp entry on your own or get them from paramchem anyway... THX for comments. It works now and I get a folder called cgenff-2b7.ff like what we seen in the share/top folder for other FF. that's too complicated to real use. Initially, I thought that the output for the ligand should be a single .itp file like what we found in Swissparam. Probably one can consider improve this script. As far as I know the CGenFF website can export full parameters for the ligand even it is already exist in CGenFF off line files. In this cases, the output file fro CGenFF website is independent from the offline FF and it already has complete necessary information for paramters and topology). Probably one can consider improve this script and export the output file as a single .itp file. 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] About topology for cyclic petide
Dear justin Thank you for your Previous reply I Have Successfully constructed topology for cyclic peptide using spce bond and Other Appropriate Changes in the . top files Yet I Want to make CO Terminal But When I interactively Choose the Terminal By pdb2gmx It Shows Only 1)COO - 2)COOH 3)None I want to Make One more Choice Namely CO For C-Terminal Residue of (LAst Residue ) My Cyclic Peptide It Adds One Two oxygen atom on the Carbon Atom (O1 O2) . But I Need the Addition Of One Oxygen Atom How to Do It ? Which Database file Should I EDIT ? .C Terminal Data Base Thanks In Advance -- 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] About topology for cyclic petide
On 12/26/12 9:50 AM, vidhya sankar wrote: Dear justin Thank you for your Previous reply I Have Successfully constructed topology for cyclic peptide using spce bond and Other Appropriate Changes in the . top files Yet I Want to make CO Terminal But When I interactively Choose the Terminal By pdb2gmx It Shows Only 1)COO - 2)COOH 3)None I want to Make One more Choice Namely CO For C-Terminal Residue of (LAst Residue ) My Cyclic Peptide It Adds One Two oxygen atom on the Carbon Atom (O1 O2) . But I Need the Addition Of One Oxygen Atom How to Do It ? It sounds like you made the wrong choice. The proper selection is None such that your C-terminus is treated like any internal residue and is engaged in a peptide bond with the N-terminus. The actual bond in this case is defined in specbond.dat since pdb2gmx can only otherwise handle linear sequences of residues. Which Database file Should I EDIT ? .C Terminal Data Base You don't need to edit anything, you only need to use the terminus selection mechanism correctly. -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] g_dih calculation doubt
On 12/26/12 12:57 AM, Kavyashree M wrote: Dear users, I was using g_dih to find the phi/psi transitions of a protein along the trajectory using the following command - g_dih -f a.xtc -s a.tpr -o dihout.out -b x -e y -w When it started running it indicated many of the following lines Dihedral around 7793,7804 not found in topology. Using mult=3 what does it mean..? they are not nearby atoms so as to calculate dihedral angle.. Clearly g_dih thinks they are. Refer to your coordinate or topology files to find out what those atoms are. A difference of only 11 atoms is not very large. They could indeed be in the same residue or in a disulfide. At the end it gave the dihedral transitions of each residue along the trajectory - it displayed - Calculated all dihedrals, now analysing... and then it took backup of all residue transitions creating new xvg files of the same residues. I compared the two files ie, the backup file and the corresponding new file there was drastic differences why is there difference between these two files although both are plots of degrees v/s time. Backup files are generated after multiple invocations of a command. Apparently whatever you ran multiple times produced different output. One more question is some times it shows dihedral values of more than 360.. sometimes 1000 etc.. does it mean that the bond has undergone rotation so many times.. I am sorry I am not getting this. Also the file that it generates does not say which is phi/psi specifically. So I suppose 2nd column is phi and 3rd column is psi? it it right? You'll have to provide snippets of your output, with complete .xvg header information here. Most files are very well labeled so as to make the columns obvious. -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] Convert .psf to .top
Hi, in vmd there is a package called topotools ( https://sites.google.com/site/akohlmey/software/topotools). This package has the magic command writegmxtop. Be carefull 'cause the created .top might miss some information (tipically angles and dihedrals) so I advice you to carefully check the .top file. Francesco 2012/12/26 Kieu Thu Nguyen kieuthu2...@gmail.com Dear All, Are there any method that can convert CHARMM PSF files to Gromacs topology files ? Thank for any help ! Best regards, KT -- 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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 convert CGenFF into .itp file?
On 2012-12-26 13:00, Albert wrote: On 12/26/2012 12:39 PM, Peter C. Lai wrote: It should come with two files. A .prm file, which contains the actual forcefield parameters that you use the script to convert to bonded and nonbonded .itp and atomtypes.atp The .rtf file is the charmm equivalent of our .rtp file: it contains some premade residue topologies with charge and connectivity information. I don't know if there are scripts to convert this or not, but it's easy enough to get what you need by hand especially since if your ligand isn't in there, you'll have to create the .rtp entry on your own or get them from paramchem anyway... THX for comments. It works now and I get a folder called cgenff-2b7.ff like what we seen in the share/top folder for other FF. that's too complicated to real use. Initially, I thought that the output for the ligand should be a single .itp file like what we found in Swissparam. Probably one can consider improve this script. As far as I know the CGenFF website can export full parameters for the ligand even it is already exist in CGenFF off line files. In this cases, the output file fro CGenFF website is independent from the offline FF and it already has complete necessary information for paramters and topology). Probably one can consider improve this script and export the output file as a single .itp file. Hey, it's open source. Let us know how it goes :). best Albert -- 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] how to convert CGenFF into .itp file?
On 12/26/2012 07:53 PM, David van der Spoel wrote: Hey, it's open source. Let us know how it goes you can simple create an account and login https://www.paramchem.org/ after your login, click upload molecule in left panel. Now you will see the option: Include parameters that are already in CGenFF tick this option and the server will generate a full version of ligand topology which could be independent from the offline CGenFF. Now what we need is just improve the script and convert it into a single .itp file into Gromacs. I think this would be the best solution. Here is an example output for Methanol molecule from CGenFF --example-- * Toppar stream file generated by * CHARMM General Force Field (CGenFF) program version 0.9.6 beta * For use with CGenFF version 2b7 * read rtf card append * Topologies generated by * CHARMM General Force Field (CGenFF) program version 0.9.6 beta * 36 1 ! penalty is the highest penalty score of the associated parameters. ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 ! and 50 mean some basic validation is recommended; penalties higher than ! 50 indicate poor analogy and mandate extensive validation/optimization. RESI 8870.000 ! param penalty= 0.000 ; charge penalty= 0.000 GROUP! CHARGE CH_PENALTY ATOM O OG311 -0.651 !0.000 ATOM C CG331 -0.039 !0.000 ATOM H1 HGA30.090 !0.000 ATOM H2 HGA30.090 !0.000 ATOM H3 HGA30.090 !0.000 ATOM H4 HGP10.420 !0.000 BOND OC BOND OH4 BOND CH1 BOND CH2 BOND CH3 END read param card flex append * Parameters generated by analogy by * CHARMM General Force Field (CGenFF) program version 0.9.6 beta * ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 ! and 50 mean some basic validation is recommended; penalties higher than ! 50 indicate poor analogy and mandate extensive validation/optimization. BONDS CG331 OG311 428.00 1.4200 ! PROT methanol vib fit EMB 11/21/89 CG331 HGA3322.00 1.1110 ! PROT alkane update, adm jr., 3/2/92 OG311 HGP1545.00 0.9600 ! PROT EMB 11/21/89 methanol vib fit; og tested on MeOH EtOH,... ANGLES OG311 CG331 HGA3 45.90108.89 ! PROT MeOH, EMB, 10/10/89 HGA3 CG331 HGA3 35.50108.405.40 1.80200 ! PROT alkane update, adm jr., 3/2/92 CG331 OG311 HGP1 57.50106.00 ! Team Sugar, HCP1M OC311M CC331M; unchanged DIHEDRALS HGA3 CG331 OG311 HGP1 0.1800 3 0.00 ! og methanol IMPROPERS END RETURN -- 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_dih calculation doubt
Unfortunately, g_dih was written before 1997 and its documentation is very poor. It does not actually read the connectivity in the .tpr file, nor does it attempt to infer connectivity other than for some protein backbone dihedrals. For some reason, it thinks it finds some for your topology, but can't find parameters for them (wherever it imagines it should find them). As far as I can see, its functionality is entirely duplicated by g_angle, so g_dih will probably be removed in 4.6. I suggest you use g_angle for whatever you are trying to do. Mark On Wed, Dec 26, 2012 at 4:31 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/26/12 12:57 AM, Kavyashree M wrote: Dear users, I was using g_dih to find the phi/psi transitions of a protein along the trajectory using the following command - g_dih -f a.xtc -s a.tpr -o dihout.out -b x -e y -w When it started running it indicated many of the following lines Dihedral around 7793,7804 not found in topology. Using mult=3 what does it mean..? they are not nearby atoms so as to calculate dihedral angle.. Clearly g_dih thinks they are. Refer to your coordinate or topology files to find out what those atoms are. A difference of only 11 atoms is not very large. They could indeed be in the same residue or in a disulfide. At the end it gave the dihedral transitions of each residue along the trajectory - it displayed - Calculated all dihedrals, now analysing... and then it took backup of all residue transitions creating new xvg files of the same residues. I compared the two files ie, the backup file and the corresponding new file there was drastic differences why is there difference between these two files although both are plots of degrees v/s time. Backup files are generated after multiple invocations of a command. Apparently whatever you ran multiple times produced different output. One more question is some times it shows dihedral values of more than 360.. sometimes 1000 etc.. does it mean that the bond has undergone rotation so many times.. I am sorry I am not getting this. Also the file that it generates does not say which is phi/psi specifically. So I suppose 2nd column is phi and 3rd column is psi? it it right? You'll have to provide snippets of your output, with complete .xvg header information here. Most files are very well labeled so as to make the columns obvious. -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] how to convert CGenFF into .itp file?
On 2012-12-26 20:29, Albert wrote: On 12/26/2012 07:53 PM, David van der Spoel wrote: Hey, it's open source. Let us know how it goes Sorry what I meant was: If you make a better version of the charmm2gromacs script, then please upload it to the website. Cheers, David. you can simple create an account and login https://www.paramchem.org/ after your login, click upload molecule in left panel. Now you will see the option: Include parameters that are already in CGenFF tick this option and the server will generate a full version of ligand topology which could be independent from the offline CGenFF. Now what we need is just improve the script and convert it into a single .itp file into Gromacs. I think this would be the best solution. Here is an example output for Methanol molecule from CGenFF --example-- * Toppar stream file generated by * CHARMM General Force Field (CGenFF) program version 0.9.6 beta * For use with CGenFF version 2b7 * read rtf card append * Topologies generated by * CHARMM General Force Field (CGenFF) program version 0.9.6 beta * 36 1 ! penalty is the highest penalty score of the associated parameters. ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 ! and 50 mean some basic validation is recommended; penalties higher than ! 50 indicate poor analogy and mandate extensive validation/optimization. RESI 8870.000 ! param penalty= 0.000 ; charge penalty= 0.000 GROUP! CHARGE CH_PENALTY ATOM O OG311 -0.651 !0.000 ATOM C CG331 -0.039 !0.000 ATOM H1 HGA30.090 !0.000 ATOM H2 HGA30.090 !0.000 ATOM H3 HGA30.090 !0.000 ATOM H4 HGP10.420 !0.000 BOND OC BOND OH4 BOND CH1 BOND CH2 BOND CH3 END read param card flex append * Parameters generated by analogy by * CHARMM General Force Field (CGenFF) program version 0.9.6 beta * ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 ! and 50 mean some basic validation is recommended; penalties higher than ! 50 indicate poor analogy and mandate extensive validation/optimization. BONDS CG331 OG311 428.00 1.4200 ! PROT methanol vib fit EMB 11/21/89 CG331 HGA3322.00 1.1110 ! PROT alkane update, adm jr., 3/2/92 OG311 HGP1545.00 0.9600 ! PROT EMB 11/21/89 methanol vib fit; og tested on MeOH EtOH,... ANGLES OG311 CG331 HGA3 45.90108.89 ! PROT MeOH, EMB, 10/10/89 HGA3 CG331 HGA3 35.50108.405.40 1.80200 ! PROT alkane update, adm jr., 3/2/92 CG331 OG311 HGP1 57.50106.00 ! Team Sugar, HCP1M OC311M CC331M; unchanged DIHEDRALS HGA3 CG331 OG311 HGP1 0.1800 3 0.00 ! og methanol IMPROPERS END RETURN -- 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] Dangling bond at terminal end of RNA rosetta model
Hi everybody, Im trying to use GROMACS for MD of a RNA model generated by Rosetta (FARFAR). As a test I try processing a modelledpdb file. When I prepare thetopology files (pdb2gmx -f test.pdb -ff amber99 -ignh ) from pdb I encounter following output : Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/amber99.ff/aminoacids.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/amber99.ff/dna.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/amber99.ff/rna.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/amber99.ff/aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/amber99.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.12# Processing chain 1 'A' (165 atoms, 8 residues) Identified residue rG1 as a starting terminus. Identified residue rC8 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION 4.5.5 Source code file: pdb2top.c, line: 1031 Fatal error: There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- When processing the corresponding structure from the pdb database (2IXZ)all files are generated as expected. I tried to compare the de novo model with the experimentally determined one but I cant find the problem(all terminal residues seem to have the same amountof atoms when ignoring the hydrogen atoms). I dont have a clue where to look next. Anyone got a clueto solve this issue? Thanks in advance, Kind regards, Gert -- 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] Convert .psf to .top
Thank Francesco :-) On Wed, Dec 26, 2012 at 11:31 PM, francesco oteri francesco.ot...@gmail.com wrote: Hi, in vmd there is a package called topotools ( https://sites.google.com/site/akohlmey/software/topotools). This package has the magic command writegmxtop. Be carefull 'cause the created .top might miss some information (tipically angles and dihedrals) so I advice you to carefully check the .top file. Francesco 2012/12/26 Kieu Thu Nguyen kieuthu2...@gmail.com Dear All, Are there any method that can convert CHARMM PSF files to Gromacs topology files ? Thank for any help ! Best regards, KT -- 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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] merge .gro, .top files
Do you mean that i have to add the line sed '2s/^.*$/'$(wc -l file.gro)'/' file.gro out.gro into the old script merge.py ? On Wed, Dec 26, 2012 at 6:39 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi KT, To update the number of atoms in a merged .gro file, assuming a single frame and no empty lines after the box definition, you have to replace the second line with the number of lines minus three: sed '2s/^.*$/'$(wc -l file.gro)'/' file.gro out.gro Cheers, Tsjerk On Tue, Dec 25, 2012 at 7:33 AM, Kieu Thu Nguyen kieuthu2...@gmail.com wrote: But i don't see file gromacs_topology_merger.py in the web Vedat gave me. Tsjerk, can you give me the script for updating the number of atoms ? I searched in google, but i have not found it yet. It's really my stupid question, but i don't know why. Thanks ! Best regards, KT On Tue, Dec 18, 2012 at 6:43 PM, Kieu Thu Nguyen kieuthu2...@gmail.com wrote: thank all so much :-) KT On Tue, Dec 18, 2012 at 4:12 PM, Vedat Durmaz dur...@zib.de wrote: there's also an executable topology merger available written in python called gromacs_topology_merger.py as part of a the software package ZIBMolPy designed for conformational analysis at https://github.com/CMD-at-ZIB/**ZIBMolPy https://github.com/CMD-at-ZIB/ZIBMolPy given (in the same directory) a topology file topol.top (argument 1) and two (or more) itp files mol1.itp and mol2.itp included in the top file, the tool writes out a new topology file (argument 2) merging the first two molecules from the include sequence of which itp files are given. note: the number of molecules to be merged should be 1 in the [ molecules ] section. if one of them is meant to appear multiple times in the merged topology, the process needs to be repeated accordingly. vedat Am 18.12.2012 09:38, schrieb Erik Marklund: 18 dec 2012 kl. 09.30 skrev Tsjerk Wassenaar: Hi KT, If you mean concatenating frames in .gro files, you can use trjcat or just cat. If you mean merging the coordinates, it's a wee bit more complicated. Since you also ask for top files, I guess that's the case. Here's a snippet of python code that will do the trick: #!/usr/bin/env python import sys f = [open(i).readlines() for i in sys.argv[1:]] print Merged gro file\n%5d % (sum([len(i) for i in f]) - 3*len(f)) print .join([.join(i[2:-1]) for i in f]), print f[0][-1] For the top files, it is necessary to ensure all the moleculetypes are #included, and that the [ molecules ] listing under [ system ] has the right number and order of the molecules in the merged gro file. There's no tool for that that I know of. In principle you could use grompp for checking that. It would print out a heap of warinngs/notes/errors if structure file and topology don't match. Erik Cheers, Tsjerk On Tue, Dec 18, 2012 at 6:18 AM, Kieu Thu Nguyen kieuthu2...@gmail.com wrote: Dear All, I don't know which tools used to merge 2 files .gro, 2 files .top ? Can i use trjcat ? Thanks ! KT -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/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_Lists http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/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_Lists http://www.gromacs.org/Support/Mailing_Lists --**- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/**elflab/index.html http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] Dangling bond at terminal end of RNA rosetta model
On 12/26/12 6:32 PM, Gert Peters wrote: Hi everybody, Im trying to use GROMACS for MD of a RNA model generated by Rosetta (FARFAR). As a test I try processing a modelledpdb file. When I prepare thetopology files (pdb2gmx -f test.pdb -ff amber99 -ignh ) from pdb I encounter following output : Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/amber99.ff/aminoacids.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/amber99.ff/dna.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/amber99.ff/rna.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/amber99.ff/aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/amber99.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.12# Processing chain 1 'A' (165 atoms, 8 residues) Identified residue rG1 as a starting terminus. Identified residue rC8 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION 4.5.5 Source code file: pdb2top.c, line: 1031 Fatal error: There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- When processing the corresponding structure from the pdb database (2IXZ)all files are generated as expected. I tried to compare the de novo model with the experimentally determined one but I cant find the problem(all terminal residues seem to have the same amountof atoms when ignoring the hydrogen atoms). I dont have a clue where to look next. Anyone got a clueto solve this issue? The most common issue is residue name. Terminal nucleic acids are named, e.g., RG5 to indicate 5' terminus. Similarly, RG is an internal residue and RG3 is a 3' terminal residue. -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] merge .gro, .top files
On 12/26/12 7:46 PM, Kieu Thu Nguyen wrote: Do you mean that i have to add the line sed '2s/^.*$/'$(wc -l file.gro)'/' file.gro out.gro into the old script merge.py ? sed is a standard *nix command, issued from the command line. -Justin On Wed, Dec 26, 2012 at 6:39 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi KT, To update the number of atoms in a merged .gro file, assuming a single frame and no empty lines after the box definition, you have to replace the second line with the number of lines minus three: sed '2s/^.*$/'$(wc -l file.gro)'/' file.gro out.gro Cheers, Tsjerk On Tue, Dec 25, 2012 at 7:33 AM, Kieu Thu Nguyen kieuthu2...@gmail.com wrote: But i don't see file gromacs_topology_merger.py in the web Vedat gave me. Tsjerk, can you give me the script for updating the number of atoms ? I searched in google, but i have not found it yet. It's really my stupid question, but i don't know why. Thanks ! Best regards, KT On Tue, Dec 18, 2012 at 6:43 PM, Kieu Thu Nguyen kieuthu2...@gmail.com wrote: thank all so much :-) KT On Tue, Dec 18, 2012 at 4:12 PM, Vedat Durmaz dur...@zib.de wrote: there's also an executable topology merger available written in python called gromacs_topology_merger.py as part of a the software package ZIBMolPy designed for conformational analysis at https://github.com/CMD-at-ZIB/**ZIBMolPy https://github.com/CMD-at-ZIB/ZIBMolPy given (in the same directory) a topology file topol.top (argument 1) and two (or more) itp files mol1.itp and mol2.itp included in the top file, the tool writes out a new topology file (argument 2) merging the first two molecules from the include sequence of which itp files are given. note: the number of molecules to be merged should be 1 in the [ molecules ] section. if one of them is meant to appear multiple times in the merged topology, the process needs to be repeated accordingly. vedat Am 18.12.2012 09:38, schrieb Erik Marklund: 18 dec 2012 kl. 09.30 skrev Tsjerk Wassenaar: Hi KT, If you mean concatenating frames in .gro files, you can use trjcat or just cat. If you mean merging the coordinates, it's a wee bit more complicated. Since you also ask for top files, I guess that's the case. Here's a snippet of python code that will do the trick: #!/usr/bin/env python import sys f = [open(i).readlines() for i in sys.argv[1:]] print Merged gro file\n%5d % (sum([len(i) for i in f]) - 3*len(f)) print .join([.join(i[2:-1]) for i in f]), print f[0][-1] For the top files, it is necessary to ensure all the moleculetypes are #included, and that the [ molecules ] listing under [ system ] has the right number and order of the molecules in the merged gro file. There's no tool for that that I know of. In principle you could use grompp for checking that. It would print out a heap of warinngs/notes/errors if structure file and topology don't match. Erik Cheers, Tsjerk On Tue, Dec 18, 2012 at 6:18 AM, Kieu Thu Nguyen kieuthu2...@gmail.com wrote: Dear All, I don't know which tools used to merge 2 files .gro, 2 files .top ? Can i use trjcat ? Thanks ! KT -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/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_Lists http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/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_Lists http://www.gromacs.org/Support/Mailing_Lists --**- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/**elflab/index.html http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search
Re: [gmx-users] Dangling bond at terminal end of RNA rosetta model
On Thu, Dec 27, 2012 at 12:32 AM, Gert Peters gert.pet...@ugent.be wrote: Hi everybody, Im trying to use GROMACS for MD of a RNA model generated by Rosetta (FARFAR). As a test I try processing a modelledpdb file. When I prepare thetopology files (pdb2gmx -f test.pdb -ff amber99 -ignh ) from pdb I encounter following output : Sorting it all out... Opening force field file /usr/local/gromacs/share/** gromacs/top/amber99.ff/**aminoacids.hdb Opening force field file /usr/local/gromacs/share/** gromacs/top/amber99.ff/dna.hdb Opening force field file /usr/local/gromacs/share/** gromacs/top/amber99.ff/rna.hdb Opening force field file /usr/local/gromacs/share/** gromacs/top/amber99.ff/**aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/** gromacs/top/amber99.ff/**aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.12# Processing chain 1 'A' (165 atoms, 8 residues) Identified residue rG1 as a starting terminus. Identified residue rC8 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully --**- Program pdb2gmx, VERSION 4.5.5 Source code file: pdb2top.c, line: 1031 Fatal error: There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/**Documentation/Errorshttp://www.gromacs.org/Documentation/Errors --**- When processing the corresponding structure from the pdb database (2IXZ)all files are generated as expected. I tried to compare the de novo model with the experimentally determined one but I cant find the problem(all terminal residues seem to have the same amountof atoms when ignoring the hydrogen atoms). I dont have a clue where to look next. AMBER parameterizes the terminal residues differently from the non-terminal residues. See rna.rtp. That requires that the terminal residues have a different residue name that pdb2gmx can match accordingly. With the information we have, nobody can say why one of your input files works and the other doesn't. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_dih calculation doubt
Thanks both of you for the suggestions. Regarding the backup files - I did not run the command multiple times. Thank you kavya On Thu, Dec 27, 2012 at 1:01 AM, Mark Abraham mark.j.abra...@gmail.comwrote: Unfortunately, g_dih was written before 1997 and its documentation is very poor. It does not actually read the connectivity in the .tpr file, nor does it attempt to infer connectivity other than for some protein backbone dihedrals. For some reason, it thinks it finds some for your topology, but can't find parameters for them (wherever it imagines it should find them). As far as I can see, its functionality is entirely duplicated by g_angle, so g_dih will probably be removed in 4.6. I suggest you use g_angle for whatever you are trying to do. Mark On Wed, Dec 26, 2012 at 4:31 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/26/12 12:57 AM, Kavyashree M wrote: Dear users, I was using g_dih to find the phi/psi transitions of a protein along the trajectory using the following command - g_dih -f a.xtc -s a.tpr -o dihout.out -b x -e y -w When it started running it indicated many of the following lines Dihedral around 7793,7804 not found in topology. Using mult=3 what does it mean..? they are not nearby atoms so as to calculate dihedral angle.. Clearly g_dih thinks they are. Refer to your coordinate or topology files to find out what those atoms are. A difference of only 11 atoms is not very large. They could indeed be in the same residue or in a disulfide. At the end it gave the dihedral transitions of each residue along the trajectory - it displayed - Calculated all dihedrals, now analysing... and then it took backup of all residue transitions creating new xvg files of the same residues. I compared the two files ie, the backup file and the corresponding new file there was drastic differences why is there difference between these two files although both are plots of degrees v/s time. Backup files are generated after multiple invocations of a command. Apparently whatever you ran multiple times produced different output. One more question is some times it shows dihedral values of more than 360.. sometimes 1000 etc.. does it mean that the bond has undergone rotation so many times.. I am sorry I am not getting this. Also the file that it generates does not say which is phi/psi specifically. So I suppose 2nd column is phi and 3rd column is psi? it it right? You'll have to provide snippets of your output, with complete .xvg header information here. Most files are very well labeled so as to make the columns obvious. -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://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/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_Lists 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
