AMBER: Potential of mean force.

From: Catein Catherine <>
Date: Fri, 08 Jun 2007 20:01:42 +0800

Dear Jerome and other PMF experists,

Thank you very much! I did the calculations.

I did the PMF calculations accordingly, however, when I tried to do the PMF
along a distance form 1 to 40 A), but keeping the angle unchanged with the
corrected input files below. As I want the drug move away from the receptor
along a 1-D axis, I did a series of umbrella sampling MD runs with the
following restrainst.

Angle Distance
180.0 1.0
180.0 2.0
180.0 3.0
180.0 4.0
180.0 40.0

While the distances were changing from 1.0 to 40.0A as expected, the angle
also changed from 120.0 to 230.0, even I keep using the same restaint at
180.0 for all the umbrella sampling MD runs.

Is it just normal?

Can I still use the distance histogram for the PMF calculations but ingoring
the changes in angles?

Should I keep increasing the force constant for the angle restraint untill
the angle don't vary at all?

Please kindly share your experiences with me.



>Subject: Re: AMBER: How to fix two angle but do umberlla sampling
>Date: Thu, 07 Jun 2007 17:38:26 +0200
>Your procedure seems OK, you can put various restaint in a simple rst
>However, in your restraint file, "iat" is supposed to correspond to the
>atom number in your pdb file.
>If you want to restraint the distance between the first 2 atoms of your
>structure, you should have :
>For an angle restraint you should have 3 atoms (ex iat=1,2,3) and 4 for
>a dihedral (iat=7,8,9,10)
> > # fixed angle restrainst
> >
> > &rst iat=4,5,5 r1=-180.0, r2=180.0, r3=180.0, r4=180.0, rk2 = 1000.0,
>rk3 =
> ^^^^^^^
>here I don't understand why you write 5,5
> > &rst iat=4,5,5,5 r1=0.0, r2=0.0, r3=0.0, r4=360.0, rk2 = 1000.0, rk3 =
> ^^^^^^
>look at your PDB and write the good atom numbers. There is no need to
>add additional inforamtion on the atom name (at least on AMBER 8.0,
>maybe it changed for A9, but I don't see why)
>Good lick
>Jerome Golebiowski, PhD
>LCMBA, team Chemometrics and Molecular Modeling
>University of Nice, parc Valrose
>06108 Nice Cedex2 France
>tel : +33 (0)4 92 07 61 03
>The AMBER Mail Reflector
>To post, send mail to
>To unsubscribe, send "unsubscribe amber" to

Learn English via Shopping Game, FREE!

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Jun 10 2007 - 06:07:37 PDT
Custom Search