Can you perform a simulation of the chromophore alone? Does that stay stable?
Gerrit > Date: Sat, 13 Nov 2010 12:32:04 -0800 > From: Ramachandran G <gtr...@gmail.com> > Subject: Re: [gmx-users] GFP chromophore topology help > To: jalem...@vt.edu, Discussion list for GROMACS users > <gmx-users@gromacs.org> > Message-ID: > <aanlktintrxh3pq2xfduyzw5xtzgvtygdssra+yrec...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > 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-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 >>>> >>> >>> >>> >> >> -- >> ======================================== >> >> 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-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 >> > > > ------------------------------ > > -- > 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! > > End of gmx-users Digest, Vol 79, Issue 102 > ****************************************** -- Gerrit Groenhof MPI biophysical chemistry Goettingen Germany http://wwwuser.gwdg.de/~ggroenh/ -- 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
