Re: [gmx-users] The charge of cofactor and ligand
On 9/24/13 7:16 AM, aixintiankong wrote: Dear prof. The format of parameters is convenient to the software of Amber and not to gromacs. if i use the parameters i must use some tools to convert it to the itp format for gromacs. so i use acpype to get itp format. i just doubt that i use amber99sb for protein and AM1-BBC for ligand and resp charge for cofactor. it looks like unprofessional and i don't know whether can affect the the MD . I do like this is right or not ? The best method is to follow published protocols rather than trying make something up that you hope will be right. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] The charge of cofactor and ligand
Dear prof, can i use the RESP charge for the cofactor NAD+ and AM1-BBC charge for ligand and then use acpype to generate GAFF force field parameter for the NAD+ and ligand? -- 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] The charge of cofactor and ligand
How do GAFF and acpype work? Mark On Mon, Sep 23, 2013 at 5:47 PM, aixintiankong aixintiank...@126.com wrote: Dear prof, can i use the RESP charge for the cofactor NAD+ and AM1-BBC charge for ligand and then use acpype to generate GAFF force field parameter for the NAD+ and ligand? -- 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] The charge of cofactor and ligand
On 9/23/13 5:10 PM, aixintiankong wrote: Dear, First i use UCSF Chimera to add hydrogens and AM1-BCC charges for the NAD+ and a ligand. when i check the charge of NAD+, I find that the distribution of charge is not correct, the N1N atom should be positive charge but the chimera give a negative. so i copy the resp charge form http://www.pharmacy.manchester.ac.uk/bryce/amber and then replace the AM1-BCC with the resp charge formhttp://www.pharmacy.manchester.ac.uk/bryce/amber . At last, i use acpype –i ben.mol2 –c user to get the nad.itp file. so the NAD+ use the RESP charge and the ligand use the AM1-BCC charges , can i do like this ? i use this method to get the NAD+.itp file? is correct or not ? Why not just use the parameters that are already published? Unless there's something wrong with them, there's no need to reinvent the wheel. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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
