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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 03 2016 - 10:30:02 PDT
