AMBER Archive (2004)

Subject: Re: AMBER: Residue Loading Problem

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.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

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 ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to