From: Yarrow Madrona (amadrona_at_uci.edu)
Date: Sat Mar 09 2013 - 17:54:03 CST
I apologize in advance for my newbie question.
I am trying to compile a top_all_22_prot_HEME.inp parameter and topology
file for a P450 enzyme by adding published HEME/thiol parameters (The
Compound I of Nitric Oxide Synthase: The Active Site Protonation State.
Shaik et al). I then planned to run psfgen with these files.
I have read the tutorials on the parameter and topology files but the only
thing I find for the Fe-S are "dummy parameters". My question is how does
NAMD know what the forces should be if they are not listed? This is taken
from the authors supplemental section on Heme parameters. I have attached
the supplemental material and listed an exert below. Thank you for your
FE S 000.000 0.0000
FE OT 000.000 0.0000
! for Oxo
FE O 000.000 2.0000
O H 300.000 1.0000
O O 000.000 1.5000
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