[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
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
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
