ok sir..
On Thu, Jun 23, 2011 at 4:06 PM, Ramachandran G <gtr...@gmail.com> wrote: > Hi, > That is the problem. Yet i do not know whether it is working fine > not.....i have been working with that for nearly 9-10months but not > satisfied yet. > In the following mail i will cut and paste the force field parameters which > you can use it with amber. If you have time please go ahead and modify > according to your wish. > > Regards, > Rama > > > > On Wed, Jun 22, 2011 at 11:27 PM, bharat gupta > <bharat.85.m...@gmail.com>wrote: > >> 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 >> >> >> -- >> 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