AMBER Archive (2006)

Subject: Re: AMBER: acidifying a water box

From: David A. Case (case_at_scripps.edu)
Date: Thu Sep 14 2006 - 17:21:01 CDT

On Thu, Sep 14, 2006, Eric Shamay wrote:

> I'm attempting to model a water/D2O system (298 molecules each) with varying
> levels of HCl. I'm not sure exactly how to pursue this in AMBER (7.0), but
> I've taken the following approach which causes sander to crash during a
> minimization:

You have atoms on top of each other in the pdb file, for example:

ATOM 1 D1 d2o 1 0.957 0.000 0.000
ATOM 2 D2 d2o 1 -0.240 0.927 0.000
ATOM 3 O d2o 1 0.000 0.000 0.000
TER
ATOM 4 D1 d2o 2 0.957 0.000 0.000
ATOM 5 D2 d2o 2 -0.240 0.927 0.000
ATOM 6 O d2o 2 0.000 0.000 0.000

These two waters are superimposed, which leads to divide-by-zero errors
in sander. You will have to fix this before continuing -- looks like it might
be just a trivial(?) error in the script used to create the starting
structure.

....good luck...dac

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