Dear Sir, It will be of great help to send the force field. actually I want to know whether it was working fine for u or not ?? ... Pls send the file and if it's working fine then I think you can deposit it in User contributions in gromacs repository...
On Thu, Jun 23, 2011 at 2:38 PM, Ramachandran G <gtr...@gmail.com> wrote: > Why you are doing simulation without chromophore? Chromophore is important > in GFP. If you want i can send you the forcefield which i am using for GFP. > > Rama > > > On Wed, Jun 22, 2011 at 10:29 PM, bharat gupta > <bharat.85.m...@gmail.com>wrote: > >> Hi Sir, >> >> Actually I am doing the simulation without the chromophore. So, planarity >> does not matter to be .. >> >> >> >> On Thu, Jun 23, 2011 at 2:23 PM, Ramachandran G <gtr...@gmail.com> wrote: >> >>> Hi Bharat, >>> I used Amber force field, but still i am not statisfied with the >>> parameters which i used because after some nanosecond simulation(1 -2 ns) >>> the planarity of the sturcture changes. I tired changing the force >>> constant but still not much successfull. If you got success please let me >>> know. >>> >>> with regards, >>> Rama >>> >>> On Wed, Jun 22, 2011 at 10:11 PM, bharat gupta <bharat.85.m...@gmail.com >>> > wrote: >>> >>>> Hi, >>>> >>>> I want to simulate a docked complex of my protein (GFP) with >>>> phosphotyrosine. I have found this - ffG43a1p forcefield contains >>>> parameters >>>> for pTYR, so I want to know how good is this FF for simulating my system... >>>> As in the literature its mentioned that people have used CHARMM, AMBER, >>>> OPLS >>>> ff for simulation of GFP. So, using this will be a correct choice or not >>>> ... >>>> >>>> -- >>>> Room No. : 7202A, 2nd Floor >>>> Biomolecular Engineering Laboratory >>>> Division of Chemical Engineering and Polymer Science >>>> Pusan National University >>>> Busan -609735 >>>> South Korea >>>> Lab phone no. - +82-51-510-3680, +82-51-583-8343 >>>> Mobile no. - 010-5818-3680 >>>> E-mail : monu46...@yahoo.com >>>> >>>> >>>> -- >>>> gmx-users mailing list gmx-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 >>>> >>> >>> >>> >>> -- >>> Postdoctoral Research Scholar, >>> Department of Chemistry, >>> University of Nevada, Reno. >>> >>> -- >>> gmx-users mailing list gmx-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 >>> >> >> >> >> -- >> Bharat >> Ph.D. Candidate >> >> Room No. : 7202A, 2nd Floor >> Biomolecular Engineering Laboratory >> Division of Chemical Engineering and Polymer Science >> Pusan National University >> Busan -609735 >> South Korea >> Lab phone no. - +82-51-510-3680, +82-51-583-8343 >> Mobile no. - 010-5818-3680 >> E-mail : monu46...@yahoo.com >> >> >> -- >> gmx-users mailing list gmx-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 >> > > > > -- > Postdoctoral Research Scholar, > Department of Chemistry, > University of Nevada, Reno. > > -- > gmx-users mailing list gmx-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 > -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com
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