Re: [gmx-users] ffamber updates
Hi Eric Thanks for doing that great job concerning the amberFF for GROMACS. I recently came across this paper: http://www.biophysj.org/cgi/content/abstract/92/11/3817?maxtoshow=HITS=10hits=10RESULTFORMAT=searchid=1FIRSTINDEX=0volume=92firstpage=3817resourcetype=HWCIT There Perez et al refined new alpha/gamma angles for nucleic acids. They claim, that these dihedrals in the original amber99 lead to irreversible transitions, which have an influence on the correct conformation of NA-strands. I thought about including them in the amber99-GROMACS port, but maybe it's better if you do, because you have more experience in building the amber-ports. What do you think? I didn't read the paper according to your 99sb-port yet. Do you think it makes sense to switch from the amber99 to amber99sb? Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Eric J. Sorin wrote: Hi GROMACS users, We've updated our ffamber ports to include the AMBER-99SB force field. Please visit the new website for information and downloads: http://chemistry.csulb.edu/ffamber/. Eric ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ffamber updates
Hi Maik, These updated NA params would be nice to add and test, but I've been too busy lately to do this. I'd like to get to it soon though (i.e. this year ;o) As for AMBER-99SB, the paper makes reasonable arguments I think, but I've not run any real test or production runs with 99SB myself, so I can't comment on it w.r.t. any specific systems. Eric - Original Message - From: Maik Goette [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org; [EMAIL PROTECTED] Sent: Friday, September 28, 2007 2:57 AM Subject: Re: [gmx-users] ffamber updates Hi Eric Thanks for doing that great job concerning the amberFF for GROMACS. I recently came across this paper: http://www.biophysj.org/cgi/content/abstract/92/11/3817?maxtoshow=HITS=10hits=10RESULTFORMAT=searchid=1FIRSTINDEX=0volume=92firstpage=3817resourcetype=HWCIT There Perez et al refined new alpha/gamma angles for nucleic acids. They claim, that these dihedrals in the original amber99 lead to irreversible transitions, which have an influence on the correct conformation of NA-strands. I thought about including them in the amber99-GROMACS port, but maybe it's better if you do, because you have more experience in building the amber-ports. What do you think? I didn't read the paper according to your 99sb-port yet. Do you think it makes sense to switch from the amber99 to amber99sb? Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Eric J. Sorin wrote: Hi GROMACS users, We've updated our ffamber ports to include the AMBER-99SB force field. Please visit the new website for information and downloads: http://chemistry.csulb.edu/ffamber/. Eric ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] ffamber updates
Hi GROMACS users, We've updated our ffamber ports to include the AMBER-99SB force field. Please visit the new website for information and downloads: http://chemistry.csulb.edu/ffamber/. Eric ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
