RE: [AMBER] Binding Energy Calculation by QM/MM method

From: Ross Walker <>
Date: Sun, 14 Mar 2010 11:13:40 -0700

> There is currently no working version of QM/MMGBSA to calculate the
> binding
> free energy in AMBER, although efforts are currently underway to
> include
> this implementation. A way for you to get around this would be to setup
> the
> unsolvated complex, receptor, and ligand mdcrds yourself, and then run
> a
> QM/MM using sander and set imin=5 to do a post-processing analysis on
> all
> three of those trajectories. You can grep out the energies and do the
> statistics analysis yourself, also.

What do you believe is the problem with using QM/MMGBSA? The QM/MM model in
AMBER supports Generalized Born it should be a simple matter to do MMGBSA
with it. Will the results be good? I have no idea but it should work right
now. You might have to hack the perl scripts a bit but that shouldn't be too

If you know of more fundamental reasons why it wouldn't work I'd be happy to
hear them and take a look.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | |

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Received on Sun Mar 14 2010 - 11:30:03 PDT
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