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 <[email protected]>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 <[email protected]> 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 >> <[email protected]>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 <[email protected]>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 < >>>> [email protected]> 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 : [email protected] >>>>> >>>>> >>>>> -- >>>>> 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 >>>>> >>>> >>>> >>>> >>>> -- >>>> Postdoctoral Research Scholar, >>>> Department of Chemistry, >>>> University of Nevada, Reno. >>>> >>>> -- >>>> 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 >>>> >>> >>> >>> >>> -- >>> 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 : [email protected] >>> >>> >>> -- >>> 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 >>> >> >> >> >> -- >> Postdoctoral Research Scholar, >> Department of Chemistry, >> University of Nevada, Reno. >> >> -- >> 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 >> > > > > -- > 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 : [email protected] > > > -- > 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 > -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno.
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