Hi
Many thanks for the reply. Regarding the preparation of files for my small ligand I followed the tutorial4b for generation of small molecule parameters using antechamber (
http://ambermd.org/tutorials/basic/tutorial4b/), I created the *.prmtop and *.inpcrd files for my ligand. However, by using the MM-PBSA calculation (tutorial A3), the result was surprising. The binding free energy for the complex of small ligand -receptor was around ~-4000kCal/mol based on GB calculations. Should I use ante-MMPBSA.py for generating of the ligand, receptor, and complex from the solvated form of complex?
ThanksMaryam
On Monday, 3 October 2016, 20:37, Bruno Falcone <brunofalcone.qo.fcen.uba.ar> wrote:
Hi, adding to what David has said, it sounds like you're probably
breaking bonds when defining the ligand. How did you generate the
parameter files? I recommend using ante-MMPBSA.py
Hope this helps,
Bruno
On 03/10/16 08:44, David A Case wrote:
> On Mon, Oct 03, 2016, Maryam Hamzehee wrote:
>
>> I am trying to do MM-PBSA calculation for determining binding energy for
>> the complex of receptor and an small ligand. I went through the MMBPSA
>> tutorial and used python-based version of MM-PBSA. Unfortunately PB did
>> not work, I ignored the PB and continued with GB. After calculation the
>> delta G was -4124.0239.
>> GENERALIZED BORN:
>> WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIALTERMS. THE
>> VALIDITY OF THESE RESULTS ARE HIGHLY QUESTIONABLE
> Please read the opening paragraphs in Chapter 31 of the Manual. You need to
> be able to these calculations "by hand" first. This is (fairly) easy with GB,
> since the averages of all the energy terms are printed in the mdout file, and
> you just need to subtract the receptor and ligand energies from that of the
> complex. This will give you results that you can compare to the results of
> the python script, to try to see where the problems are coming from.
>
> (Above ignores contributions from configurational entropy; but you need to
> tackle the big problems first.)
>
> ...good luck....dac
>
>
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Received on Tue Oct 04 2016 - 01:30:02 PDT
