AMBER Archive (2007)

Subject: Re: AMBER: Problems loading pdb file including Mg ions

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Oct 24 2007 - 12:21:43 CDT

> The problem with addition of heavy atoms was indeed because sugar
> phosphate addition - but I don't want them to be added... Actually this
> is the ligand (Adenine) and it has to remain without sugar and phosphate
> - how can I manage to tell that to LEap? It converts automatically this
> ADE to RA3 and adds sugar and phosphate...
>
> The problem of not integral charge is also due to this conversion of
> ligand adenine into terminal residue...

You need to find or create a residue template without the sugar and
phosphate, giving it a unique residue name and calculating charges
for it if creating, then change the residue name in the pdb file to
match, load the template, then load your pdb.

Bill
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