Should I need to corret charge ...??? On Thu, Nov 15, 2012 at 11:51 PM, rama david <[email protected]>wrote:
> 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 <[email protected]> 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 [email protected] >> 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 [email protected]. >> * Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > > -- 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
