Re: AMBER: Reg restraint value obtained during umbrella sampling

From: David A. Case <>
Date: Thu, 31 May 2007 13:39:39 -0700

On Thu, May 31, 2007, D.Usharani wrote:
> I am a new subscriber for amber. I am trying to do an umbrella sampling
> for a 12 base pairs two DNAs separated by certain distance using amber8.
> The reaction coordinate is along the two center of mass of DNA. The
> distance restraint file I used is according to amber8 manual (pg 173) and
> is as follows:
> &rst
> iat= -1,-1, nstep1=1, nstep2=6000,
> iresid=1,irstyp=0,ifvari=1,ninc=0,imulti=0,ir6=0,ifntyp=0,

First, try with ifvari=0, just to see if you get a restraint. Also, try
working your way up from simple constraints to more complex ones, rather than
starting with almost the most complex combination possible.

> r1=0.00000E+00, r2=112.0000, r3=112.0000, r4=99.0000,

this line is wrong, since the program needs r1<r2<=r3<r4. I don't understand
why you are not getting an error message related this.

> rk2=5.0000, rk3=5.0000,
> r1a=0.00000E+00, r2a=110.0000, r3=110.0000, r4=99.0000,

Here you are re-defining r3 and r4, and not setting r3a and r4a. Since r3a
and r4a are never set, I don't know what kind of behavior to expect...


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Received on Sun Jun 03 2007 - 06:07:28 PDT
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