AMBER Archive (2007)

Subject: AMBER: Potential of mean force.

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Fri Jun 08 2007 - 07:01:42 CDT

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.

Thanks

Cat

>From: Jerome.GOLEBIOWSKI_at_unice.fr
>Reply-To: amber_at_scripps.edu
>To: amber_at_scripps.edu
>Subject: Re: AMBER: How to fix two angle but do umberlla sampling
>fordistance?
>Date: Thu, 07 Jun 2007 17:38:26 +0200
>
>Hi,
>Your procedure seems OK, you can put various restaint in a simple rst
>file.
>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 :
>iat=1,2
>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
>--
>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
>http://www.unice.fr/lcmba
>http://www.unice.fr/lcmba/golebiowski
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