On Sat, May 18, 2013 at 1:43 PM, Debayan Chakraborty
<debayan.ch.gmail.com>wrote:
> Dear AMBER users,
> I am keen to do a stability analysis of
> various G quadruplex polymorphs using the mm_pbsa.pl available within
> AmberTools. My system consists of 716 atoms which includes two potassium
> cations. I am using the following input file for the analysis :
>
> .GENERAL
> PREFIX test
> PATH ./
> #
> COMPLEX 0
> RECEPTOR 1
> LIGAND 0
> #
> RECPT with_ions.prmtop
> #
> GC 0
> AS 0
> DC 0
> #
> MM 1
> GB 1
> PB 0
> MS 0
> #
> NM 0
> #
> .MM
> DIELC 1.0
> .GB
> IGB 1
> GBSA 1
> SALTCON 0.2
> EXTDIEL 80.0
> INTDIEL 1.0
> #
> SURFTEN 0.0072
> SURFOFF 0.0
> #
>
> I am keen to know whether I am doing it right. Unfortunately I could not
> make use of the MMPBSA.py script because everytime it complains that the
> ligand and the complex topology files are missing.
In MMPBSA.py, stability calculations are done by specifying _only_ the
complex topology files (as per instructions in the MMPBSA.py manual as well
as the example in the MMPBSA.py test suite in
$AMBERHOME/AmberTools/test/mmpbsa_py/08_Stability/
>
> Also since I am using
>
> explicit K+ ions for this analysis do I need to make any changes to the
>
> original script. I would be grateful to know if someone in the community
>
> has done similar analysis using MMPBSA ?
>
I would be skeptical about the applicability of GB in your case. You may
even have to go to the non-linear PB solver to get more reasonable results,
since you're dealing with such highly charged systems. Perhaps someone has
published a similar study to what you're attempting?
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat May 18 2013 - 18:30:03 PDT
