Hi Donnie, On Mon, 04 May 2009 12:15:23 -0700, Donnie Berkholz <[email protected]> wrote:
> On 13:58 Mon 04 May , Robert Campbell wrote: > Thanks, Rob! > > I've come across a web-based application called PepBuild that I'm using > for the moment because I only need a few right now, so manual creation > is fine. I'll give this a shot later on because I'm thinking about some > more automated testing. Come to think of it, there is also Tinker (http://dasher.wustl.edu/tinker/) which has a program called "protein" whose description is: PROTEIN A program for automated building of peptide and protein structures. Upon interactive input of an amino acid sequence with optional phi/psi/omega/chi angles, D/L chirality, etc., the program builds internal and Cartesian coordinates. Standard bond lengths and angles are assumed for the peptide. The program will optionally convert the structure to a cyclic peptide, or add either or both N- and C-terminal capping groups. Atom type numbers are automatically assigned for the specified force field. The final coordinates and a sequence file are produced as the output. You can feed this an input file (it need not be interactive) and it will very quickly generate coordinates. So if you are interested in building many structures I think it would be the fastest way. The output is in Tinker xyz format, but can be easily changed to pdb. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 Fax: 613-533-2497 <[email protected]> http://pldserver1.biochem.queensu.ca/~rlc
