Subject: Re: CCL:automatical generation of polypeptide / oligo coordinates?

From: root <[email-masked]>
Date: Sun, 1 Mar 1998 19:25:01 +0300 (MSK)

Dear CCLers,

few days ago I sent the following request for help:

>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. 

So far, I've received the followinig pointer by Paul Beroza (thanks
Paul!): 

> Hi Eugene,
>
> I wrote a program do construct polypeptide structures from the
> primary sequence and a file specifying the type of structure
> desired (extended, alpha helical, etc.).  It is written in "nab",
> a language that was developed to model large biomolecules.  You
> can find more information on David Case's web page:
>	 http://www.scripps.edu/case
>
> Paul Beroza
> CombiChem Inc.

I have not tried his package yet, as I have discovered that protein, a
part of the Tinker suite

  http://dasher.wustl.edu/tinker/

can do what I wanted (it compiles with f77 under Linux; the following
polylysine 50-mer has been made with the protein tool:
http://liposome.genebee.msu.su/gifs/polylys-50-mer-chlorides.gif
(structure not minimized yet, chloride counterions added manually).

Btw, the problems with Solvate unable to handle Corina-generated
structures had to do with the redid-id (fourth column in the pdb file) 
being zero. By setting it manually to one I have finally managed to
hydrate my nonprotein polyelectrolytes with Solvate. 

Apropos Solvate: there seems to be an atof bug in a Linux library (?) 
which makes the program scan garbage from the -t (thickness) command line
argument. Had somebody experienced similiar difficulties? (To fix it, I
think I'll either upgrade the libraries, or make a (kludgey) workaround
with (double) atoi). 

Regards,

Eugene Leitl