AMBER: MM-PBSA questions/clarifications

From: Rima Chaudhuri <>
Date: Tue, 6 Feb 2007 12:51:08 -0600

Dear Amberites,

I am a novice at MM-PBSA, trying to calculate the binding free energy of my
protein-ligand system. However, I have certain outstanding questions after
having read through the literature and going through some of the archive
messages here:
1) To generate the snapshots, does the mdcrd files have to be stripped off
water and counterions? or should this be the mdcrd out of the MD-run (with
explicit water) ? whereas the prmtop files for the lig/receptor/complex
being the unsolvated prmtops?? I could not find anything conclusive from the
archive and am left undecided.My guess is, it should be stripped? but in the
amber tutorial, I did not find any mention of it. Also, in the it mentions that the NTOTAL flag must list the total number
of atoms including water and ions, so that again confuses me, as in what
should the coordinate file be??

2) I tried using the snapshots generated from the mdcrd file with explicit
water, for the MM-PBSA-binding calculation and land up getting the error of
'No values for MM ELE existing >> ' which made me think that the snapshots
may need to be generated off the stripped co-ordinate file....please

Again, if the snapshots generated in the beginning are not from the explicit
water coordinate file, and so the following binding energy calculations,
what is the purpose of running the simulation with explicit water/periodic
boundary conditions for MM-PBSA purposes? Maybe I

thanks a lot in advance...

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Received on Wed Feb 07 2007 - 06:07:41 PST
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