Dear Sir, Thank you so much for your reply. To be specific, my system has only four lipid moities- 2 cholesteryl oleates and 2 phosphotidyl cholines. But I was not able to get all atom parameters for these lipids from the lipid book( only united atom parameters were available). So I had resorted to using united atom for the whole system. But I am afraid if I am missing out on some crucial protein-drug interactions because of this united atom consideration. Kindly guide me in this regard. Thank you so much once again.
Yours sincerely, Revathi M.S.Research Scholar Indian Institute of Technology Madras India --- On Tue, 28/5/13, David van der Spoel <[email protected]> wrote: From: David van der Spoel <[email protected]> Subject: Re: [gmx-users] choice of forcefield To: [email protected] Date: Tuesday, 28 May, 2013, 1:30 PM On 2013-05-28 14:39, massimo sandal wrote: > What other people do? Read literature. Gromacs allows you to choose many. If you need detailed results use an atomistic force field. > > > 2013/5/28 Dr. Vitaly Chaban <[email protected]> > >> In my mind, MARTINI is a decent option to build your particular topology >> upon. >> >> Dr. Vitaly Chaban >> >> >> On Tue, May 28, 2013 at 8:22 AM, Revthi Sanker <[email protected] >>> wrote: >> >>> Dear all, >>> I am a beginner to performing simulations and my system consists of >>> protein+ cholesteryl ester +phospholipid and drug. Papers involving >> lipids >>> are in general united atom, while those involving drug-protein systems >> are >>> all-atom mostly. Kindly suggest me which of these, all-atom or united >> atom >>> should I be using for my system. >>> >>> Thanks for your help in advance >>> Yours sincerely, >>> Revathi >>> M.S. Research Scholar >>> Indian Institute of Technology,Madras >>> India >>> -- >>> gmx-users mailing list [email protected] >>> 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 [email protected]. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> * Can't post? Read http://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. [email protected] http://folding.bmc.uu.se -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
