AMBER Archive (2008)

Subject: Re: AMBER: distance restraint between non-bonded molecules

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Dec 18 2008 - 13:29:30 CST

> the RST file is
> #
> # 11 ASN ND2 142 DT O4 2.5
> &rst
> ixpk= 0, nxpk= 0, iat= -1,2838, r1= 1.30, r2= 1.80, r3= 2.81, r4= 3.31,
>
> rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
> igr1= 180, 181,
> &end
> #
> # 11 ASN ND2 143 DT O4 5.5
> &rst
> ixpk= 0, nxpk= 0, iat= -1,2870, r1= 1.30, r2= 1.80, r3= 6.17, r4= 6.67,
> igr1= 180, 181,
> &end
> #
> # 69 ASN ND2 121 DT O4 2.5
> &rst
> ixpk= 0, nxpk= 0, iat= -1,2171, r1= 1.30, r2= 1.80, r3= 2.81, r4= 3.31,
> igr1=1179,1180,
> &end
> #
> # 69 ASN ND2 122 DT O4 5.5
> &rst
> ixpk= 0, nxpk= 0, iat= -1,2203, r1= 1.30, r2= 1.80, r3= 6.17, r4= 6.67,
> igr1=1179,1180,
> &end

The atoms that are restrained in the first case are atom number -1 and and
atom number 2838. This does not look so normal. It should be a positive
number. Generally I re-create the .pdb using the prmtop/inpcrd files, and
then use that .pdb file to create the RST file. 

-- 
  Ilyas Yildirim, Ph.D.
  ---------------------------------------------------------------
  = Hutchison Hall B#10          - Department of Chemistry      =
  =                              - University of Rochester      =
  = 585-275-6766 (office)        -                              =
  = http://www.pas.rochester.edu/~yildirim/                     =
  ---------------------------------------------------------------

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