Hi
I am new to structure calculations using xplor. I am using a Dual 2 GHz
PowerPC G5 m/c for my structure calculations. My protein is only 32
residues long. I noticed however that my anneal.py script took me more
that 24 hours to give me 50 structures.
I am quite certain that I have incorrectly modified my anneal.py (which I
took form one of the examples ). I wanted to add hydrogen bonding
information and i have added the following lines to my anneal.py script.
# set up NOE potential for hydrogen bonding
from noePotTools import create_NOEPot
hb = create_NOEPot("hb",file="rmad9hydrogenbond.tbl")
hb.setPotType( "soft" )
hb.setRSwitch( 0.5 )
hb.setAsympSlope( 1. )
hb.setSoftExp(1.)
hb.setThreshold(0.5)
print hb.info()
potList.append(hb)
Is this the correct way of doing it?
Also the summary of the calculations is as follows
Results for the top 50 (of 50) structures
Average values for potential terms:
type name Energy(dev) RMSD(dev) viols(dev)
PotList TOTAL 149.81(177.86) 0.426( 0.247) 22.8( 28.6)
NOEPot hb 6.95( 7.05) 0.601( 0.404) 6.7( 4.8)
NOEPot noe 58.81( 83.88) 0.054( 0.047) 1.7( 3.1)
XplorPot ANGL 45.01( 36.63) 0.537( 0.194) 9.5( 15.5)
XplorPot BOND 6.73( 9.40) 0.003( 0.002) 0.1( 0.3)
XplorPot CDIH 1.96( 3.13) 0.985( 0.759) 0.4( 0.7)
XplorPot IMPR 7.35( 7.62) 0.374( 0.191) 1.9( 2.9)
XplorPot VDW 22.99( 38.28) 2.5( 3.2)
Thanks all for your help
Sheeja.
