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]
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