From: Sumanth Jamadagni (jamads_at_rpi.edu)
Date: Thu May 21 2009 - 10:00:13 CDT
Hi,
I am new to NAMD. I am trying to run a simultion with two protein
molecules (for testing, I have not solvated the system). I wish to
constrain one protein molecule using harmonic constraints and let the
other molecule freely sample different orientations. I have attached
the 'constrained-atoms.pdb' which I am using. Essentially. the Occupancy
of the first chain/protein molecule is set to 1.00 and that of the
second chain is set to 0.00. From the error message, it appears that
the 'constraints on' line is the one causing trouble.
This is the error message I am getting.
Charm++ fatal error:
FATAL ERROR: Setting parameter constraints from script failed!
This is my execution section of the conf file.
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 50
reinitvels $temperature
#Constraints
constraints on
consexp 2
consref constrained-atoms.pdb
conskfile constrained-atoms.pdb
conskcol O
constraintScaling 1.0
Here is a section of the PDB file where I swtich from one protein to
another:
ATOM 1672 CB SER A 112 37.555 40.761 46.314 1.00 0.00
P1 C
ATOM 1673 HB1 SER A 112 37.489 40.531 47.402 1.00 0.00
P1 H
ATOM 1674 HB2 SER A 112 38.184 41.674 46.210 1.00 0.00
P1 H
ATOM 1675 OG SER A 112 36.250 40.978 45.814 1.00 0.00
P1 O
*ATOM 1676 HG1 SER A 112 35.806 41.575 46.429 1.00 0.00
P1 H
ATOM 1677 N GLU B 113 66.366 67.955 83.567 0.00 0.00
P2 N *
ATOM 1678 HT1 GLU B 113 66.545 68.912 83.795 0.00 0.00
P2 H
ATOM 1679 HT2 GLU B 113 67.152 67.566 83.087 0.00 0.00
P2 H
ATOM 1680 HT3 GLU B 113 66.184 67.434 84.401 0.00 0.00
P2 H
ATOM 1681 CA GLU B 113 65.179 67.884 82.685 0.00 0.00
P2 C
Thanks
Sumanth
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