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.
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