you should probably send your corrected restraint input file if you
want us to check it.
On 6/8/07, Catein Catherine <askamber23.hotmail.com> wrote:
>
> 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.unice.fr
> >Reply-To: amber.scripps.edu
> >To: amber.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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Received on Sun Jun 10 2007 - 06:07:37 PDT
