AMBER Archive (2004)

Subject: Re: AMBER: Residue Loading Problem

From: david.evans_at_ulsop.ac.uk
Date: Fri Dec 03 2004 - 03:41:13 CST

>
>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.top 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

I think the non-integral charge may be because you have an unbalanced
number of terminal (DX3, DX5) residues. The charges of DA, DG, DC, DT
are all -1.000, but the terminal residues are not integral, so if you
don't have 4 termini in a duplex (because your fluorescene has
replaced one of them) it doesn't balance out.
I'm surprised that this wasn't discovered and worked around by
whoever set up the system though, so I might have missed something.

Dave Evans 

--

School of Pharmacy
University of London
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