Mary,
Most users use SCALE of 2. This is equivalent to spacing of 0.5
Angstrom ... i.e. SCALE = 1/SPACING.
By the way, if you are not using the latest AmberTools release, I
strongly recommend downloading it for your project.
Ray
On Tue, Jul 23, 2013 at 10:49 PM, Jason Swails <jason.swails.gmail.com> wrote:
> 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 - 19:00:03 PDT
