From: Raja Pandian <chemistryraj.gmail.com>
Date: Thu, 30 Jun 2011 16:26:01 +0530

Dear All,

I’m working in the field of DNA-Protein interaction. I had done DNA-Protein
simulation using AMBER FF I want to calculate the binding free energy of
DNA-Protein complex. I read the MMPB-SA tutorial; it is some what hard to
understand the procedure.

Could you pls, tell me the detail procedure about MMPB-SA calculation?

I did simulation for DNA-Protein interaction using GROMACS package.
was performed for 2 ns. After equilibration, the production run was carried
out for 20 ns. The trajectories were saved for every 1 picoseconds (ps)
interval for further analysis. The trajectories were subjected to cluster
analysis based on the RMSD between each structure. Cluster analysis was
performed using the GROMOS method. The criterion of similarity for two
structures belonging to the same cluster was fixed to be RMSD value. The
RMSD cutoff value for each system is 1.7 Å. From cluster analysis, I got the
representative model (most predominant structure) for complex (DNA-Protein)
system. Using this complex structure, I want calculate binding free energy
using MMPBSA (AMBER). From this complex structure, I had split this complex
structure into ligand and receptor models.

>From this point, how can I precede my calculation…pls tell the detail things
about MMPB-SA calculation as step by step. This might be very helpful for my
further proceedings. Already I tried the tutorial procedure ($AMBERHOME/exe/
mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log), which is not working

I tried to extract the input coordinates from snapshot_com,crd using
$AMBERHOME/exe/mm_pbsa.pl extract_coords.mmpbsa > extract_coords.log, this perl
script is not extracting the snapshot_lig.crd and snapshot_rec.crd files.

If you don’t mine, pls give me your input file (format) for the MMPB-SA

With this mail I have attached the input files (snapshot_com, snapshot_lig,
snapshot_rec binding_energy.mmpbsa, and topology files). Let me know, where
am I doing mistake?

Eagerly waiting for your reply.


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Received on Thu Jun 30 2011 - 04:00:04 PDT
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