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