AMBER Archive (2006)

Subject: Re: AMBER: erroneous placement of TER card

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Thu Nov 16 2006 - 13:06:25 CST

> > > | Residue 739(atoms 11384- 11398) is in multiple molecules.
> >
> > I wonder if setting 'connect' status on the atoms before bonding
> > might solve this.
>
> Hi Bill:
>
> Can you expand on this? What would you think we should look for, and what
> should be set?

Each chain-type residue has connect0 and connect1 atoms set (as
well as the same atoms set as head & tail). CYX probably has a
connect3 atom set as the S - see the leap script that builds the
residue lib. Since CYX works for x-linking, possibly this is the
reason, i.e. leap does the right thing when it sees it, whatever
the right thing happens to be.

Bill
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