[gmx-users] About the biotin parameter.....
jalemkul at vt.edu
Thu Nov 15 22:12:26 CET 2012
On 11/15/12 2:16 PM, rama david wrote:
> Should I need to corret charge ...???
Have you read the ATB paper? Does it give you confidence in the results? How
might you evaluate whether or not the topology produces reasonable dynamics?
All of these are things to consider, particularly the last one. No one ever
said derivation of parameters was easy, and this is precisely why.
> 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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Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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