[gmx-users] New ffAMBER Ports
Fellow GROMACS users, In answer to the many messages we've received regarding ffAMBER ports for GROMACS 4.0, we've recently posted validated AMBER ports for versions 4.0.2 and 4.0.3 (http://chemistry.csulb.edu/ffamber/). I hope you find them useful! Also, we're working on several future additions to these ports, but are also happy to have others contribute to further development ... if you are interested in participating in such development, please drop me a line as we'd be grateful to have you contribute. Cheers, Eric Eric J. Sorin, Ph.D., Assistant Professor Department of Chemistry Biochemistry California State University Long Beach 1250 Bellflower Boulevard Long Beach, CA 90840-9401 Office/Lab: MLSC-233/MLSC-300 Phone: 562.985.7537 Email: eso...@csulb.edu Web: http://chemistry.csulb.edu/esorin/ ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Non integer charge for ARG and CYX?
Hi George, I just quickly checked the partial charges in ARG from the GROMACS v3.3.1 ffamber03.rtp file and the charges due indeed sum to +1, so I'm not sure why you're seeing non-integer total charge in the .rtp file it sounds like you might have a file that was modified by someone and maybe you need to update your ffamber files (?). Please tell me: Did you get these files from http://chemistry.csulb.edu/ffamber/? Which version of GROMACS are you using? Which set of ffamber ports (shown in the top of the .rtp file)? Thanks! Eric - Original Message - From: Georgios Patargias To: gmx-users@gromacs.org Sent: Thursday, May 08, 2008 4:09 AM Subject: [gmx-users] Non integer charge for ARG and CYX? Hello Sorry if I address an already covered issue. I happened to notice that adding up the ffamber03 partial charges for ARG doesnt yield +1 but ~1.6. Also, for CYX the total charge is ~0.87. Is this is a known issue? In the .itp file, pdb2gmx adds up rounded charge values (as seen in the qtot column) and so the total ARG charge comes up to +1 and for CYX 0. In .tpr, i.e. in the simulation, the full charge values are used, as they are contained in the ffamber03.rtp but grompp doesn issu warnings for non-integer total charge save for rounding errors. Thanks in advance. George Dr. George Patargias Polymer IRC Group University of Leeds Leeds, LS2 9JT, UK ___ 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
[gmx-users] ffAMBER ports updated
Hi, We have updated the ffAMBER website to include AMBER ports for v3.3.1 and also incorporated the AMBER-03 force field of Duan et al. in all ffAMBER ports (v3.1.4 thru v3.3.1). Please visit http://folding.stanford.edu/ffamber/ for more info. Enjoy! Eric J. Sorin Pande Group Stanford University Department of Chemistry ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
