trouble running metalloprotein simulation from literature

From: Sibo Lin (sibolin_at_caltech.edu)
Date: Sat May 15 2010 - 14:44:40 CDT

• Next message: Jeffrey Potoff: "Re: Generate psf files from Scott Feller's lipid coordinates"
• Previous message: Dai, Jian1: "Generate psf files from Scott Feller's lipid coordinates"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hello, I want to simulate iron-sulfur proteins. To get started, I
succsesfully worked through the ubiquitin NAMD tutorial. But when I
try to run the build and simulation scripts for a metalloprotein
reported by Chris Chang
(http://pubs.acs.org/doi/suppl/10.1021/ct800342w), I get an error
during the simulation:

FATAL ERROR: CAN'T FIND BOND PARAMETERS FOR BOND FEJO - NR2 IN PARAMETER FILES
[0] Stack Traceback:
  [0] vsprintf+0x80 [0xb74d7700]

Can anyone help?

I suspect that my version of psfgen is generating bonds where they
should not exist, so if the solution is to manually go through the psf
file and remove all FEJO - NR2 bonds, can someone give an overview of
how to do that?

Thanks so much!
-Sibo

• Next message: Jeffrey Potoff: "Re: Generate psf files from Scott Feller's lipid coordinates"
• Previous message: Dai, Jian1: "Generate psf files from Scott Feller's lipid coordinates"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:55:47 CST