Thanks Bharatham
That means I should do implicit simulation at 50 & 55 degree celcius but
I have wet lab data that protein have optimum activity at pH 5. So if I
do implicit MD which will be at neutral pH then it will not correlated
with wet lab data that is the problem.
On 2014-05-26 21:18, Bharatham, Nagakumar wrote:
> Hello Sangita,
>
> Please don't come to conclusions that constant pH will work only with 25 degree cel. Prof. David case suggested to get some experience with implicit solvent models first before working on constant pH method. Earlier we (me and Dr. Don Bashford) compare constant pH and conventional GB methods for a protein system which provided similar conclusions in most cases. If your system is considerably big you need to add some kind of conformational sampling method such as aMD to assist sampling.
>
> P.S. Dr.Don could you please provide your insights which will provide more clear picture here.
>
> Regards,
> Kumar
> ________________________________________
> From: Sangita Kachhap [sangita.imtech.res.in]
> Sent: Monday, May 26, 2014 9:47 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] MD at constant pH and high temperature. .
>
> Thanks for reply.
>
> I have to do two different simulation at pH 5 & temperature 50 and pH 5
> & temperature 55 degree celcius. I don't have to do for range of
> temperature. So I was asking that is it possible to do MD at higher
> temperature at pH 5.
>
> Now I got the answer that constant pH is for 25 degree celcius.
>
> Is there any option to do MD at above two condition.
>
> On 2014-05-26 19:28, David A Case wrote:
> On Sun, May 25, 2014, Sangita Kachhap wrote: Is it possible to do MD simulation at constant pH and temperature range 50-55 degree Celsius simultaneously? The thermostats in Amber allow you to specify a single (target) temperature, not a range of temperatures. If you really need a range, I'm guessing you would have to run a series of simulations at various temperatures of interest, and average the results. But a single simulation at the center of you temperature range would be a good place to start. The implicit solvent GB models in Amber were parameterized for 25 C; I don't know of any work testing these at higher temperature. If you are new to Amber (or to constant pH simulations) I'd recommend getting some experience with implicit solvent models first, before trying more difficult calculations. ....dac _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber [1] [1]
With regards
--
Sangita Kachhap
SRF
C/O Dr. Balvinder Singh
BIC
IMTECH
Links:
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[1] http://lists.ambermd.org/mailman/listinfo/amber [1]
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With regards
--
Sangita Kachhap
SRF
C/O Dr. Balvinder Singh
BIC
IMTECH
Links:
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Received on Mon May 26 2014 - 09:30:03 PDT
