Subject: automatical generation of polypeptide / oligo coordinates?

From: root <[email-masked]>
Date: Tue, 24 Feb 1998 21:03:11 +0300 (MSK)

Dear CCLers,

I'm fairly certain there is a program/script capable of generating a
polypeptide / oligo e.g. in linear conformation just from the primary
structure (amino acid sequence) data somewhere out there. Corina-generated
structures from SMILES seem to lack important data, preventing both XPLOR
and Solvate from reading them (? -- feel free to correct me). I wanted to
generate pdb/psf pairs 10-30 residue-oligos for subsequent MD runs. 

In the CCL archive there seems to be no mentioning of such an animal,
which is strange.

Before I start reinventing the wheel: anybody aware of such a thing? It
can be an XPLOR script, but a simple language such as C/Perl/Python would
be preferable.

Regards,

Eugene Leitl

P. S. When compensating protein polyelectrolyte (e.g. polylysine)
      charges with counterions (e.g. chloride) is using HETATM the
      canonical thing to do, or do ATOMs suffice?

P. P. S. Anybody knows why RasMol chooses to kill CONECT when saving a
         just-read pdb file?