Subject: Re: CCL:torsion constraints in autodock

From: Margaret Johnson <[email-masked]>
Date: Thu, 11 Apr 2002 15:54:31 -0700 (PDT)

Hi Xiaojian,

The hardtorcon command doesn't work for me either. It would be great if
someone out there has some suggestions.

I'm not quite sure of the structure you're talking about there. When you
run deftors, usually the default is to have the -a flag on, which
tells the program to automatically set amide bond torsions as inactive.
If it's not an amide bond then you could try leaving it inactive.

If there's a reason why you do want the torsion semi-flexible and not
fixed, the only way I've been able to do this, so far, is to use
"gausstorcon" with a high energy barrier, e.g. 100 or higher, and small
half-width, e.g. 10-20 degrees. This usually gives a variation of about
+/- 5 degrees in the torsion. I don't know how/when this barrier is
applied in the calculation though.

>
> I wondered whether I gave the wrong constraint. For a
> torsion A-B-C-D, in autodock program, the rotatable bond is defined by two
> atoms(B-C), then where the A and D come from, and is it possible to assign
> the torsion angle unambiguously in the constraints? How to do that?

I think the program uses general conventions for defining torsions... for
example, if there are two possible heavy atoms, it would use the one with
higher priority to define the torsion, e.g. O rather than C. But I'm not
sure about that. However, you can check this using your output structures,
as the torsion angles in the final structure are printed out in the output
(.dlg) file.

The actual value of the torsion angle is defined relative to the starting
torsion angle. For example, if you want the torsion to stay near where it
is in the starting structure, you would set it to zero, and also set the
dihe0 value to 0. instead of random in the .dpf file.

Best regards,

Maggie

Margaret A. Johnson
Dept. of Chemistry
Simon Fraser University
Burnaby, B.C.
Canada V5A 1S6
Tel. (604) 291-5650
Fax. (604) 291-3765
E-mail: [email-masked]