Re: AMBER: Reg restraint value obtained during umbrella sampling

From: D.Usharani <>
Date: Fri, 1 Jun 2007 22:42:23 +0530 (IST)

Dear David,

  I realised the mistakes in the input file. so i tried doing the centre
of mass distance restraint for two alanine residues seperated by 20
angstroms and the input for restraint is

   iat= -1,-1, nstep1=1, nstep2=5000,
   r1=0.00000, r2=20.0000, r3=20.0000, r4=99.0000,
      rk2=1.0000, rk3=1.0000,
   igr1 = 1,0,
  grnam1 (1) ='CA',
   igr2 = 2,0,
  grnam2 (1) ='CA',

I defined the ifvari =0 but still it didnt gave any restraint value in
the out put file. It reads the restraint but not the r1,r2,r3,r4 and rk2
and rk3 values.
          Begin reading energy term weight changes/NMR restraints
 DUMPFREQ 10 0 0.000000 0.000000 0 0
                         ** No weight changes given **

 Requested file redirections:
  DISANG = distcom.RST
  DUMPAVE = umb.20
 Restraints will be read from file: distcom.RST
 Here are comments from the DISANG input file:

 COM ( -1)-COM ( -1) NSTEP1= 1 NSTEP2=
R1 = 0.000 R2 = 0.000 R3 = 0.000 R4 = 0.000 RK2 = 0.000 RK3 =
 Rcurr: NAN Rcurr-(R2+R3)/2: NAN MIN(Rcurr-R2,Rcurr-R3): NAN
                       Number of restraints read = 1

                  Done reading weight changes/NMR restraints

For a simple system like alanine even a simple distance restraint is
sufficient but for the 12 base pairs DNA how to do it?

 So I tried the simple distance restraint value with near by atom of COM
of the individual DNA, then it has read the restriant and gave DUMPAVE
values also, but by this DNA's get opened up after certain windows.

So i would like to know what more modifications are needed in the
distance restraint file?

Thanks in advance

> 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...
> ...dac
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c/o Prof E.D.Jemmis
Inorganic and PhysicalChemistry
Indian Institute of Science
Bangalore -560012
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Received on Sun Jun 03 2007 - 06:07:38 PDT
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