James, PyMOL's peptide & small molecular builder is no more rigorous that a handheld plastic model. Unfortunately, DeLano Scientific doesn't have the developer "bandwidth" right now to get into the simulations business. Instead, we hope to facilitate and encourage integration with existing external packages via PyMOL wizards and simple Python glue.
Thus, our near-term goal with the builder is to simply provide scientists like yourself with a user interface for building molecules and setting up *initial* poses that will then be subjected to rigorous computations external to PyMOL. There are plenty of integrations options out there, from free and/or open-source tools like GROMACS, APBS, Tinker, ArgusLab, GAMESS US, and MMTK, to academic codes like Amber, Charmm, Dock, and Autodock, to commercial codes like Szybki (MMFF), Fred, Glide, BatchMin, MOE, Sybyl, or Discover. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Jim Nettles > Sent: Monday, August 15, 2005 8:56 AM > To: James R. Graham > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Builder Question > > Hello James, > > There is really a lot of room for discussion regarding your > questions. > Considering peptide conformations is complicated business and > there is generally not "a" structure. There is great > conformational flexibility even for small, constrained, > cyclic peptides. As for the MD - yes, a classical MD > trajectory is entirely determined by the starting structure. > One can introduce random number seeds, high temperature, etc > ... to explore greater space, but where you start is > definitely worthy of thoughtful consideration. > > I can send references and more discussion off list, if you > are interested. > > Cheers, > > Jim N. > ________________________________________________________ > James Nettles, Ph. D. Computational Pharmacology > Liotta/Snyder Group, Modeling Division, Department of > Chemistry Emory University 1515 Pierce Dr. Atlanta, Ga. 30322 > jnet...@emory.edu TEL: (404)966-4617 FAX: (404)728-0991 > ________________________________________________________ > > On Aug 15, 2005, at 11:36 AM, James R. Graham wrote: > > > Hello All, > > > > How "physiological" are the structures that are produced > from builder? > > Meaning, how are the angles, etc. determined? Might such a > resulting > > structure mimic a chemically-synthesized peptide? > > > > I have taken peptides I created using builder and done some MD > > simulations and the structures certainly change, but I > wonder whether > > the changes are limited by the initial starting > structure...which is, > > of course, a question for another mailing list, I suppose. ;) > > > > james > > > > > > ------------------------------------------------------- > > SF.Net email is Sponsored by the Better Software Conference & EXPO > > September 19-22, 2005 * San Francisco, CA * Development Lifecycle > > Practices Agile & Plan-Driven Development * Managing > Projects & Teams > > * Testing & QA Security * Process Improvement & Measurement * > > http://www.sqe.com/bsce5sf > > _______________________________________________ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & > EXPO September 19-22, 2005 * San Francisco, CA * Development > Lifecycle Practices Agile & Plan-Driven Development * > Managing Projects & Teams * Testing & QA Security * Process > Improvement & Measurement * http://www.sqe.com/bsce5sf > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > >
