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] 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
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] 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
