AMBER Archive (2009)

Subject: Re: [AMBER] 1-4 vdW, GB MM difference

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Thu Apr 16 2009 - 09:47:55 CDT

On Thu, Apr 16, 2009, Jimmy Heimdal wrote:
>
> I try to calculate MM-(PB/GB)SA energies, and get a strange 1-4 vdW
> energy difference between a GB and MM calculation.

Here's what I have found on a quick inspection:

1. I get the same results you do.

2. This sort of difference does not seem to happen with "standard" protein
or nucleic acid prmtops.

My best guess is that it has to do with the Zn ions and possible bonds
between it and its ligands. Are there such crosslinks? Can you
describe how you made the prmtop file? Could you create an example with
a much smaller protein part that shows the problem?

It does indeed look like a bug, but more information would be helpful in
tracking it down.

...regards...dac

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