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

[rama david]

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..
> 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>
>>
>> ==============================**==========
>> --
>> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>
>
>