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
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Received on Thu May 05 2011 - 14:30:05 PDT
