It sounds like you are not setting the receptor and ligand masks correctly
in the input file. You will have to manually define these variables in the
MMPBSA.py input file for the ligand and receptor residues you would like to
perform the entropy calculation on.
Good luck!
-Bill
On Thu, May 5, 2011 at 5:25 PM, mish <smncbr.gmail.com> wrote:
> Hello everyone :
>
> I have got an issue dealing with Entropy calculation using MM/PBSA.py
> script. Lets see the problem in this way:
> I have a system with 6 binding pockets so it has 6 ligands present in it. I
> ran the MD of complex (R+L1+L2+L3+L4+L5+L6) where LI to L6 are the same
> ligands. Now I am trying to do entropy calculation for each ligand (Suppose
> L1), where rest 5 will be part of receptor. Since, we have to input
> corresponding prmtop file to generate the snapshots of complex, rec and
> ligand, the script is generating wrong snapshots. Every time it had the
> same
> L6 as Lignad and R+L1-L5 receptor in generated snapshots. I wonder how can
> we deal with this case when same ligand in bound in 6 positions.
>
> Thanking U
> mish
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 05 2011 - 15:00:07 PDT
