Thank you, Justin.. I added the all the needed connectivity for GFP chromophore in the aminoacid.rtp(mentioned -C and +N to indicate the preceding and following residue) and also defined the residue as "Protein" in residuetypes.dat. For the non existing bond types, bond angles, proper and improper dihedrals, i added newly in the file ffbonded.itp. Also hydrogen atom connectivity are defined in the .hdb file.
The structure looks perfect after pdb2gmx but when i do minimization, the atoms(N+ and C-) chromphore along with neighbouring residue terminals are flying apart. So i don't know where i am making mistakes. Should i need to give information in the Termini database flie *.tdb ? or Is this due to wrong force constant values? or Is my force field parameter has mistakes? Thank your for you help. Rama On Fri, Nov 12, 2010 at 6:20 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Ramachandran G wrote: >> >> Thank you for the help. >> I have successfully constructed the chromphore molecule but >> still have problem in connecting it to the neigbhouring residues. I >> don't know how the connection sequence needs to be given in gromacs. >> Please help >> > > You stand a much better chance of getting useful help if you at least > describe what you attempted and why it didn't work. For the GFP > chromophore, which incorporates into the backbone, you need to add > connectivity in the .rtp file like any other amino acid residue (-C and +N), > and define the residue as "Protein" in residuetypes.dat (if using version > 4.5.x). Without knowing what you've done, though, I'm only guessing. > > -Justin > >> with regards, >> Rama >> >> On Tue, Nov 9, 2010 at 3:22 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: >>> >>> Ramachandran G wrote: >>>> >>>> Dear gromacs users: >>>> >>>> I have constructed the Amber03 force fields parameters >>>> (bonds,angles, proper and imporer dihedral.....) for the chromophore >>>> (p-hydroxybenzylidene-imidazolinone) inside GFP system and got the >>>> topology. But after energy minimization of the system, the >>>> conformation of the chromophore totally changed and the benzene and >>>> imidazole ring got puckered although i did not got any error message. >>>> >>> No Gromacs tool will check your work for you. It will do what you tell >>> it. >>> Likely you omitted some necessary bonded parameters (bonds, angles, >>> impropers, etc). Either that, or the parameters you supplied produce the >>> incorrect behavior. >>> >>> -Justin >>> >>>> Could anyone help me? Thank you. >>>> >>>> >>>> with regards, >>>> Rama >>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> -- >>> gmx-users mailing list gmx-us...@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 >>> >> >> >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-us...@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 > -- 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
