Justin,
thanks again for explanation. I'll try find other possible more automatic ways for conversion of the itp to rtps. If I've success I'll post here :) James tin Lemkul <jalem...@vt.edu>: > > > On 12/5/12 11:46 AM, James Starlight wrote: >> >> Justin, >> >> >> So as I understood such problems might be with all proteins consisted >> of prostetic groups ( Rhodopsin, myoglobin etc). Is there more trivial >> way to obtain parametrized models of such proteins with gromacs force >> fields if I have itp's of the prostetic groups made by external >> software ? >> > > In general, a prosthetic group that is not bound covalently is handled by > .itp files, anything covalently attached is handled by .rtp entries. If you > have an .itp file for a covalently bound compound, then you need to convert > it to .rtp using the contents of the .itp. After all, everything we're > talking about is topological information, just in different formats. > > -Justin > > >> >> Thanks for help >> >> James >> >> 2012/12/5 Justin Lemkul <jalem...@vt.edu>: >>> >>> >>> >>> On 12/5/12 11:19 AM, James Starlight wrote: >>>> >>>> >>>> Justin, >>>> >>>> The GFP protein consist of chromophore group which matured after >>>> folding of that protein. That prostetic group is the cyclized >>>> derivative of the Ser-Tyr-Gly peptide which is the part of the >>>> alpha-helix of that protein surrounded by the beta-barell interiour. >>>> >>>> So I want to make simulation of such protein consisted of covalently >>>> bonded prostetic group. I've made parametrisation of that isolated >>>> chromophore but couldn't integrate it into GROMOS force field because >>>> aminoacids.rtp didnt work with ITP file produced by PRODRG. It's also >>>> inportant that different mutants of GFP consist of different types of >>>> that chromophores so manual conversion of the ITP to RTP formats in >>>> each cases ( I'd like to simulate different mutants) would be very >>>> routinely. >>>> >>> >>> I don't know of a way to convert .itp files into .rtp entries, though it >>> could probably be done. The time investment in developing such a script >>> may >>> not be worth it, since creating an .rtp entry is rather simple following >>> the >>> guide in the manual and existing entries (i.e. amino acids). The choice >>> (script vs. manual effort in a text editor) is up to you. I've done >>> similar >>> things with other people before, so it's certainly possible, though a bit >>> tedious, especially for the GFP chromophore since there are lots of atoms >>> involved. I worked with it several years ago and I simply did it by hand >>> using the parameters that were suggested to you earlier for CHARMM. >>> >>> -Justin >>> >>> >>>> >>>> James >>>> >>>> 2012/12/5 Justin Lemkul <jalem...@vt.edu>: >>>>> >>>>> >>>>> >>>>> >>>>> On 12/5/12 11:00 AM, James Starlight wrote: >>>>>> >>>>>> >>>>>> >>>>>> Hi Bharat, >>>>>> >>>>>> That simulation have been done in charmm program so the convertion >>>>>> from charmm to gromacs would be more routinely for me. >>>>>> >>>>>> >>>>> >>>>> I think it would be better if you describe exactly what you need help >>>>> with. >>>>> If it's a matter of having parameters in CHARMM format but not Gromacs >>>>> format, then all you need is to follow the manual to implement the >>>>> parameters. If you're having a specific problem along the way, please >>>>> describe it fully and specifically, otherwise the default response is >>>>> "everything's in the manual and elaborated on at the webpage you >>>>> already >>>>> quoted." >>>>> >>>>> -Justin >>>>> >>>>> -- >>>>> ======================================== >>>>> >>>>> Justin A. Lemkul, Ph.D. >>>>> Research Scientist >>>>> 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. >>> Research Scientist >>> 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. > Research Scientist > 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! * 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? 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