AMBER Archive (2004)

Subject: Re: AMBER: Residue Loading Problem

From: Furse, Kristina Elisabet (
Date: Fri Dec 03 2004 - 01:23:05 CST

> Created a new atom named: C within residue: .R<CF 14>
> Created a new atom named: 6O1 within residue: .R<CF 14>
> Added missing heavy atom: .R<CF 14>.A<16O 72>
> Added missing heavy atom: .R<CF 14>.A<5C 40>

Leap didn't like the two cases where an atom name began with a number--16O and
5C. It read the 5C as C and the 16O as 6O1, so it couldn't match them up. I
changed the atom names in the prep and pdb file to 5Cc (5Cb was taken...) and
O16b, and the missing atom problem went away.

The charge problem is something else...
I got an overall charge for your pdb of -29.307900 when the pdb was read without
complaint. I don't think the problem is with the fluoescein, though. If I check
the charges in the prep file (just by doing saveamberparm CF junk.crd)
leap gives a total charge of -4.000000. I'm a protein kind of person--never work
with DNA, so maybe the answer to that one will jump out at someone else!


Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
Email: kristina.e.furse_at_Vanderbilt.Edu
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