On Tue, Jul 23, 2013 at 3:21 AM, Mary Varughese <maryvj1985.gmail.com>wrote:
> Sir,
>
> I want to calculate binding energy of a nucleic acid ligand complex
> (explicit simulation , TIP3Pbox) using mm_pbsa.pl script.
> many values are explained for the input parameters
>
> It would be helpful if you can suggest the appropriate values
>
> * SCALE- lattice spacing in no of grids per angstrom. what value should i
> choose?
>
Not sure on this one. If it was me doing the study, I would look at other
authors performing PB calculations on nucleic acids and look at their grid
spacing (especially useful would be a study that mentions why that value
was chosen or even better a systematic discussion of which values are
sufficient).
> * INP
> *SURFTEN and SURFOFF
>
The default values of INP and SURFTEN/SURFOFF are probably best.
> * IGB
> *GBSA
>
I think this has been discussed on a previous thread (maybe even one of
yours, I can't remember). To reiterate the point, do _not_ use GB on a
nucleic acid system. It is known to perform badly and I would not trust
any results obtained from it.
> i dont understand which values should i choose and its significance.
>
> Also could i put MM= PB= GB= MS=1 to get binding energy without entropy and
> then again run the program with NM=1 to get the entropy calculation?
>
Yes, you can do that.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jul 23 2013 - 08:00:04 PDT
