Hi Justin thank you,
The ATB server link for Biotin are as follow.. http://compbio.biosci.uq.edu.au/atb/download.py?molid=5783 compbio.biosci.uq.edu.au/atb/download.py?molid=2212 Now should I need to do QM calculations, free energy simulations, and empirical refinement. What is your opinion on these topics. Is there any free available software for these work???( I never did any QM calclation, Sorry for these basic Question). With Best Wishes and Regards, Rama David. On Thu, Nov 15, 2012 at 8:23 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/15/12 9:47 AM, rama david wrote: > >> Hi Gromacs Friends, >> >> I want to do the simulation of system containing the >> biotin. >> I know that the charge calculated by prodrg is not good. >> I want to use the GROMOS96 53a6 force field or OPLS force field. >> ( 1st choice is GROMOS second choice is OPLS) >> >> Please would you tell me how to get topologies for biotin with correct >> charge. >> >> > Most molecules in the Gromos force fields can be reasonably built from the > charge group building blocks. For biotin, the only trick is the thioether > functional group, but perhaps there are parameters for that. I know there > has been a lot of recent work expanding the Gromos force fields, so someone > may have done that already. > > If suitable parameters aren't available, you need to read the primary > literature for the parameter set you're using and derive parameters in a > suitable way, which for Gromos would typically involve some preliminary QM > calculations, free energy simulations, and empirical refinement. The ATB > server is also a possibility; it performs much better than PRODRG, but > anything you get from an automated server should be validated first before > being used in any simulation you care about. > > -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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
