Hello Warren,
Thanks for the response.
That is exactly what I have done--taken structures produced with
builder and brought them into GROMACS and have obtained minimized
structures, but as Jim Nettles mentioned, such techniques can depend
on what the initial structure is, so I was just wondering whether
there were any constraints placed upon amino acids as they are placed
that might mimic chemical synthesis methods. I know it's quite a
reach, but thought I'd ask anyway. ;)
james
On Aug 15, 2005, at 12:12 PM, Warren DeLano wrote:
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
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