AMBER Archive (2003)

Subject: Re: AMBER: mgbjsb radii in GBSA

From: David A. Case (case_at_scripps.edu)
Date: Mon Nov 10 2003 - 10:10:17 CST

On Mon, Nov 10, 2003, Giulio Rastelli wrote:

> >> I include a prep file of a molecule that did NOT work, as an example.
> >>
> >> 0 0 2
> >>
> >> This is a remark line
> >> molecule.res
> >> <1> XYZ 0
> >> CORRECT OMIT DU BEG
> >> 0.0000
> >> 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
> >> 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
> >> 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
> >> 4 O18 o M 3 2 1 1.540 111.208 180.000 -0.604
> >> 5 C12 c M 4 3 2 1.219 123.332 167.874 0.131
> >> 6 O19 o E 5 4 3 1.219 119.978 153.351 -0.604

This looks like a bad prep file. Can you say what commands you used to
create this? A prep file with the "XYZ" attribute (also known as "prepc"
in antechamber) should not have dummy atoms. Try using the "prepi" rather
than the prepc format, and see if that helps. (The prepc format used to
be broken in other respects...I'm not sure if they got fixed or not.)

..good luck....dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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