AMBER Archive (2002)

Subject: Re:PDB file with CONECT record

From: Bill Ross (photoriot_at_yahoo.com)
Date: Mon Apr 08 2002 - 15:02:21 CDT

> I have a pdb file for a double crossover DNA
molecule
> ...with connectivity record. When I load the pdb
> file I find that xleap automatically connects more
> at the crossover (like the P is connected to O5'
> at all the crossovers going from one chain to
> other)). These connections are not in the
> connectivity record. ...
> ALso it does not keep some of its origianl
> connectivity record, Like I have nicked the two
> chains at few locations
> and have connected them with PO2 to have the
> crossovers, These connectivity records are in pdb
> file, But when I load them in xleap it does not show

> these connections. ...

Leap expects to read chains of standard residues,
with TER cards between each chain. So unless
instructed
otherwise via loadPdbUsingSeq, it will use the default
residue name mappings defined in the leaprc and
connect where appropriate according to the sequence,
the TER cards, and the connect atoms defined for the
residues.

It may be that the CONECT handling is not working,
since I expect that few people have exercised it in
any variety of permutations. Possibly it assumes atom
numbering according to their order in the file, vs.
the
chaotic numbering that can be found in many pdb's, so
one thing to check is whether the CONECT records refer

to ordinal numbering or text numbering.

Return correspondence should be directed to
ross_at_cgl.ucsf.edu

Bill Ross

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