AMBER Archive (2004)

Subject: AMBER: Problems with Carnal coordinate average

From: HL Eastwood (
Date: Mon Aug 09 2004 - 06:35:37 CDT


I'm having problems with getting carnal to output a coordinate average
in PDb format. In summary the Carnal script works only when I don;t specify a
"PDB flag"
type in the input file, i.e. in the section of the input file where I state:

COORD c1 average_pdb.out PDB;

only works when the pdb file format flag "PDB" isn;t present. when I just put:

COORD c1 average_pdb.out

it does work, but I get an average coordinate output in a format that I cannot
convert to PDB format using the ambpdb program. (I think it gives a .trj file
format, and for some reason the ambpdb program crashes out with this format).
ambpdb does work when I specify a .crd file format.

Are these just bugs or am I doing something wrong?

In short:

1. Can you explain how I can get Carnal to output a PDB file format.
2. In the absence of that, can you explain how I can convert the output I'm
to a PDB format.

many thanks

Hayden Eastwood
University of Edinburgh Chemistry Department
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