Re: [gmx-users] Cholesterol parameters (Charrm36) in GMX
On 2012-10-31 16:31, Yorquant Wang wrote: Hi GMX-users, Klauda et al (J. Phys. Chem. B, 2012, 116 (1), pp 203–210) recently provided Cholesterol parameters for Charmm FF. Does anyone have the corresponding .itp file for cholesterol in GMX style? Thanks for replying, Yukun there's a script charmm2gromacs-pvm.py on the gromacs website that you can download. Use with care. -- 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] Cholesterol parameters (Charrm36) in GMX
Hi David: I have tested the script. The input are 1 charmm topology file, 2 corresponding charmm parameter file and 3 foldername. But there are a lots of top_all***.rtf files and par_all***.prm files in toppar_c36_aug12/toppar folder, I don't know which pair is the correct pair. Could you give me a clue? The new parameter for cholesterol is stored in chol_new.str. If it is OK that I just put chol_new.str into the toppar_c36_aug12/toppar/ folder and transfer it directly. Thank you for replying! yorquant 2012/11/1 David van der Spoel sp...@xray.bmc.uu.se On 2012-10-31 16:31, Yorquant Wang wrote: Hi GMX-users, Klauda et al (J. Phys. Chem. B, 2012, 116 (1), pp 203–210) recently provided Cholesterol parameters for Charmm FF. Does anyone have the corresponding .itp file for cholesterol in GMX style? Thanks for replying, Yukun there's a script charmm2gromacs-pvm.py on the gromacs website that you can download. Use with care. -- 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-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 -- Yukun Wang PhD candidate Institute of Natural Sciences College of Life Science, Shanghai Jiao Tong University Cell phone: 13621806236. China Shanghai -- 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] Cholesterol parameters (Charrm36) in GMX
On 2012-11-01 09:47, Yorquant Wang wrote: Hi David: I have tested the script. The input are 1 charmm topology file, 2 corresponding charmm parameter file and 3 foldername. But there are a lots of top_all***.rtf files and par_all***.prm files in toppar_c36_aug12/toppar folder, I don't know which pair is the correct pair. Could you give me a clue? The new parameter for cholesterol is stored in chol_new.str. If it is OK that I just put chol_new.str into the toppar_c36_aug12/toppar/ folder and transfer it directly. Don't know. I think you need everything gromacs related that comes out. Do it in an empty directory. Thank you for replying! yorquant 2012/11/1 David van der Spoel sp...@xray.bmc.uu.se On 2012-10-31 16:31, Yorquant Wang wrote: Hi GMX-users, Klauda et al (J. Phys. Chem. B, 2012, 116 (1), pp 203–210) recently provided Cholesterol parameters for Charmm FF. Does anyone have the corresponding .itp file for cholesterol in GMX style? Thanks for replying, Yukun there's a script charmm2gromacs-pvm.py on the gromacs website that you can download. Use with care. -- 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-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 -- 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
