Re: [AMBER] mmpbsa input parameters

From: Ray Luo <rayhuangluo.gmail.com>
Date: Wed, 24 Jul 2013 15:31:53 +0800

As for GBSA, you may want to do an investigation on how different versions (by using different igb values) perform for your specific system.

Ray Luo, Ph.D.

On 2013-7-24, at 12:50, Mary Varughese <maryvj1985.gmail.com> wrote:

> Sir,
>
> Thank you very much for the suggestions
> I am using ambertols12. hope its ok.
> Also MMGBSA is not suitable for nucleic acid systems. Isnt?
>
>
> thanking you
> mary
>
>
> On Wed, Jul 24, 2013 at 7:29 AM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
>
>> 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
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Wed Jul 24 2013 - 01:00:03 PDT
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