Hi Jasaon,
Thanks for ur kind reply...I could not find an option in AMBERTOOL
manual for setting up 'non-linear' equation..How to do non-linear PB
calculation...? Wat I have that when I included the saltcon=0.1, the
MMGBSA value becomes close to MMPBSA..
Thanks
Rajesh
On Tue, 13 Sep 2011 20:43:17 -0400
Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, Sep 13, 2011 at 7:48 PM, Rajesh Raju
><rajesh.raju.mail.chem.tamu.edu
>> wrote:
>
>> Dear AMBER users,
>>
>> I have done mmpbsa binding free energy calculations on a 10-mer DNA
>> structures using MMPBSA.py script. The MMGBSA binding free energy
>> value changes from -43 kcal mol-1 to -60 kcal mol when included the
>> saltcon parameter (saltcon=0.1). But the MMPBSA value doesnt show
>>any
>> significant change. only about ~0.5-0.7 kcal mol-1. what is the
>> actural role of the saltcon as we are neutrilzaing the system before
>> we do simulation..?
>>
>
> The saltcon is a debye screening parameter which theoretically
>approximates
> the electrostatic screening induced by counterions. Explicit
>neutralizing
> ions should *NOT* be included in implicit solvent calculations
>unless they
> are functional and you do it very carefully. The formula for GB is
>found in
> the Amber manual, I think, and also explicitly in the references
>cited in
> the Amber manual (I remember a particularly good one by Bashford and
>Case,
> IIRC, and Onufriev has some good ones out there, too).
>
>For PB, try using the non-linear equation and see how that affects
>your
> results. Note that GB's treatment of nucleic acid electrostatics
>are highly
> suspect. NAs are highly charged systems, and GB has known problems
>when
> used on them. I would suggest searching the literature for how
>others
> approached similar problems.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Tue Sep 13 2011 - 18:30:02 PDT
