AMBER Archive (2006)

Subject: Re: AMBER: bad connectivity - more detail

From: David A. Case (case_at_scripps.edu)
Date: Fri Dec 29 2006 - 02:15:16 CST

On Wed, Dec 27, 2006, Seth Lilavivat wrote:

> "set RA.1 connect0 RA.1.P" seems to work OK, leap gives no reply and the head of
> each residue is joined by the P correctly. "set RA.1 connect1 RA.1.O2*" and
> leap replies with:
>
> set: Improper number of arguments!
> usage: set <container> <parameter> <object>
> or: set default <parameter> <value>

If you use the "desc" command to examine your residue, you will find that
Amber is using IUPAC names for the sugar atoms, (that is O2') rather than
Brookhaven/PDB names (like O2*). So, use the Amber/IUPAC name.

[If you examine files like leaprc.ff99, you will see that LEaP is converting
the names found in pdb files to its internal standards. Other programs, like
ambpdb, reverse this change on output.]

...good luck...dac

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