AMBER Archive (2007)

Subject: Re: AMBER: Implicit/Explicit solvation

From: David A. Case (case_at_scripps.edu)
Date: Wed Nov 21 2007 - 10:46:19 CST

On Wed, Nov 21, 2007, Eddie Men wrote:

> I am trying to run an implicit/explicit solvation calculation, and my
> input is that in the manual.
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 NaN NaN 0.0000E+00 N 1
>
> BOND = 515.0425 ANGLE = 1263.6023 DIHED =
> 4672.6459
> VDWAALS = ************* EEL = -35804.5153 EPB

The van der Waals energy is extremely large, such that you probably have atoms
on top of each other (or nearly so). You can use the check command in ptraj
to look for this. Try to minimize first without any PB correction to see if
that helps, but you may have to figure out why you got the bad contact in the
first place.

...dac

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