[gmx-users] About the biotin parameter.....
ramadavidgroup at gmail.com
Thu Nov 15 20:16:56 CET 2012
Should I need to corret charge ...???
On Thu, Nov 15, 2012 at 11:51 PM, rama david <ramadavidgroup at gmail.com>wrote:
> Hi Justin thank you,
> The ATB server link for Biotin are as follow..
> 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 <jalemkul at 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
>>> 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
>> 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 A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
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