Subject: AutoDock3.0: Constraining torsion

From: Susanna P Alho <[email-masked]>
Date: Fri, 10 Mar 2000 15:52:10 +0200 (EET)

Hi all,

I would like to constrain torsions in a ligand using AutoDock 3.0
simulated annealing. I've been testing the system with the following
input-file parameters concerning torsions:

# Initial Translation, Quaternion and Torsions 
tran0 10.82 26.69 25.08      #initial coordinates/A or "random" 
quat0 random                 # initial quaternion or"random" 
ndihe 5                      # number of initial torsions
dihe0 0. 0. 0. 0. 0. 	     # initial torsions

# Initial Translation, Quaternion and Torsion Step Sizes and Reduction
Factors 
tstep 0.2               # translation step/A
qstep 5.0		# quaternion step/deg
dstep 5.0               # torsion step/deg
trnrf 1.		# trans reduction factor/per cycle
quarf 1.                # quat reduction factor/per cycle 
dihrf 1.                # tors reduction factor/cycle

barrier 1000 
gausstorcon 1 0. 10.  # constrain torsion, num., angle(deg),range(deg) 
gausstorcon 2 0. 10.  # constrain torsion, num., angle(deg),range(deg 
gausstorcon 3 0. 10.  # constrain torsion, num., angle(deg),range(deg) 
gausstorcon 4 0. 10.  # constrain torsion, num., angle(deg),range(deg) 
gausstorcon 5 0. 10.  # constrain torsion, num., angle(deg),range(deg)

I've done 10 SA runs. In the outputfile there have been eight docked
conformations with  same torsional angles but in two (usually two first
ones) the angles have all been zero. What is the problem? I also tried to
change the "dihe0 0. 0. 0. 0. 0." values to bigger ones (each 20.) but
when I looked at the .dlg file I noticed that the values were enormous
after line: '5 initial torsion angles were detected...' 

I appreciate any kind of help with this issue.  

Susanna Alho 
Pharmacy student
Pharmacy Department
University of Helsinki