AMBER Archive (2007)

Subject: Re: AMBER: How to fix two angle but do umberlla sampling for distance?

From: Jerome.GOLEBIOWSKI_at_unice.fr
Date: Thu Jun 07 2007 - 10:38:26 CDT

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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