Re: [gmx-users] Re: Where is the GROMOS87 force field when using pdb2gmx
Hi, On Nov 7, 2007, at 5:40 PM, maria goranovic wrote: Thanks for the help, David. Actually, I just realized I was trying to decide based on mailing list archives which, in some cases, are 5 years old. My mistake. I will use the 43a2 field for my protein. Is there any standard procedure to combine 43a2 with the berger force field (ffgmx) for lipids ? Don't do it. The berger force field is mostly derived from OPLS, so you will (again) find it much easier to defend your choices if you mix it with OPLS-AA/L instead. Cheers, Erik ___ 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] Re: Where is the GROMOS87 force field when using pdb2gmx
Or if can use GROMOS87 for the protein and the Berger for the lipids, correct ? On Nov 8, 2007 12:49 PM, Erik Lindahl [EMAIL PROTECTED] wrote: Hi, On Nov 7, 2007, at 5:40 PM, maria goranovic wrote: Thanks for the help, David. Actually, I just realized I was trying to decide based on mailing list archives which, in some cases, are 5 years old. My mistake. I will use the 43a2 field for my protein. Is there any standard procedure to combine 43a2 with the berger force field (ffgmx) for lipids ? Don't do it. The berger force field is mostly derived from OPLS, so you will (again) find it much easier to defend your choices if you mix it with OPLS-AA/L instead. Cheers, Erik ___ 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] Re: Where is the GROMOS87 force field when using pdb2gmx
himanshu khandelia wrote: Or if can use GROMOS87 for the protein and the Berger for the lipids, correct ? Read the Berger documentation, find out what it was parameterized for use with, and see if you can use that. Nothing else is readily defensible. Mark ___ 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] Re: Where is the GROMOS87 force field when using pdb2gmx
Hi Erik, but I did read many works in the literature that used G43a*, even yours in BJ (2006). I basically agree that the 'philosophy' of the Berger lipids is derived from OPLS, thus using this latter force field is probably best suited for peptide/lipid simulation in conjunction with Berger lipids (like in Tieleman et al 2006 J. Phys.: Condens. Matter 18 S1221-S1234, or your last paper in press in Proteins). But apart from self-consistency, is it so a problem to mix Berger lipids with a GROMOS derived force field ? I ask you that because *many* previous works used Berger lipids with ffgmx (and this latter is probably still in use even if deprecated). So what is right ? It would probably be worth doing a systematic comparison of the use of different protein force fields with Berger lipids. The above ref of P. Tieleman goes in this direction. Cheers, Patrick Erik Lindahl a écrit : Hi, On Nov 7, 2007, at 5:40 PM, maria goranovic wrote: Thanks for the help, David. Actually, I just realized I was trying to decide based on mailing list archives which, in some cases, are 5 years old. My mistake. I will use the 43a2 field for my protein. Is there any standard procedure to combine 43a2 with the berger force field (ffgmx) for lipids ? Don't do it. The berger force field is mostly derived from OPLS, so you will (again) find it much easier to defend your choices if you mix it with OPLS-AA/L instead. Cheers, Erik ___ 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 thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs ___ 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] Re: Where is the GROMOS87 force field when using pdb2gmx
Thanks for the help, David. Actually, I just realized I was trying to decide based on mailing list archives which, in some cases, are 5 years old. My mistake. I will use the 43a2 field for my protein. Is there any standard procedure to combine 43a2 with the berger force field (ffgmx) for lipids ? -- Maria G. Technical University of Denmark Copenhagen ___ 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] Re: Where is the GROMOS87 force field when using pdb2gmx
maria goranovic wrote: U. Something wrong with using GROMOS87 ? I thought that was the one most commonly used for proteins ? Not really, if you look in numbers I'd guess Amber is the most popular. The G87 ff is 20 years old, and the Van Gunsteren group has already published updates in 1996 and most recently in 2005. There are known problems with it and you may indeed have problems defending your choice of force field for publications. Thanks -Maria On Nov 7, 2007 4:48 PM, maria goranovic [EMAIL PROTECTED] wrote: ___ 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] Re: Where is the GROMOS87 force field when using pdb2gmx
U. Something wrong with using GROMOS87 ? I thought that was the one most commonly used for proteins ? Thanks -Maria On Nov 7, 2007 4:48 PM, maria goranovic [EMAIL PROTECTED] wrote: ___ 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
