[gmx-users] About the biotin parameter.....

[rama david]

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 <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
>> 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>
>
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