Gas phase minimization

From: Purushottam Dixit (dixitpd_at_gmail.com)
Date: Fri Jun 15 2007 - 16:58:44 CDT

• Next message: Jonathan Lee: "heat diffusion calculation"
• Previous message: pedro.borkowski_at_utoronto.ca: "charmrun simulations over macpros"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi,

I want to put a membrane protein inside a lipid bilayer. Since the
original pdb file has missing residues, I am building residues and
performing a vacuum minimization on the membrane. During the
minimization, the tetrahedral geometries of various amino acids
(especially Arg) get affected to the point that they become
non-sensical.

Is this because I am performing gas phase minimization of a membrane
protein or is it something else?

Regards
Purushottam

• Next message: Jonathan Lee: "heat diffusion calculation"
• Previous message: pedro.borkowski_at_utoronto.ca: "charmrun simulations over macpros"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:51 CST