On Sun, Apr 27, 2014 at 7:01 AM, Sourav Purohit <sour000.gmail.com> wrote:
> Hi all,
>
> I had some doubts on the method of calculating parameters for accelerated
> MD as described in the AMBER12 manual (page no.160).
>
> 1.Does the total number of atoms (taken as 16950 in the example) include
> atoms belonging to water molecules also??
>
> 2.for the calculation of alphaD, only the number of protein residues goes
> as an input. What if a system has other components like DNA?? Should I
> include the DNA residues also??
>
> Kindly help.
>
> Thanks.
>
​Please do not double post and do not send copies of questions to our
private emails; it is inconsiderate (especially when asked on a weekend,
where people do not check emails as frequently). The reason you have not
received an answer is either:
1) Nobody knows the answer
2) Someone that does know the answer has not yet had the time to answer.
In either case, please exercise patience and wait for someone to answer.
Thanks,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Apr 27 2014 - 07:30:02 PDT
