AMBER Archive (2006)

Subject: Re: AMBER: DIST_RST

From: Cenk Andac (
Date: Tue Oct 24 2006 - 05:51:01 CDT


Here is an example for the format of RST inputs that I usually use for distance and torsion restraints. Depending on severety of distal or torsional abberations, you may want to play with boundary restraints r1, r4, rk2 and rk3 (see the DNA tutorial for limitations of the boundary forces.).

  # NOE restraint between protons HA and HB
  # For instance their atom IDs (iat) are 18,42, respectively
      ixpk= 0, nxpk= 0, iat= 18, 42,
      r1= 3.0, r2= 4.0, r3= 4.0, r4= 5.0,
      rk2=20, rk3=20, ir6=1, ialtd=0,
  #Additional NOE restraint(s) were added below in a similar format
  #for distance restraints above
  # Torsion restraint for W [O5’-C5’-C6’-N6’]
  # For instance, their atom IDs are 19,2,1,23, respectively
# W= 60 for gt, –60 for gg and 180 for tg
      iat = 19, 2, 1, 23,
    r1 = 59, r2 = 60, r3 = 60, r4 = 61,

    rk2 =3, rk3 =3,



Urszula Uciechowska <> wrote:
Hello Amber users,

I am trying to set distance restraints between some protein sidechains and a structural Zn ion.
I made a updb file and i tried to use make DIST_RST and i got such a error messages.

makeDIST_RST -upb str.upb -pdb prot.pdb -rst
 # makeDIST_RST
 Currently configured for up to 5000 atoms
 Using MAP file /usr/local/amber/dat/map.DG-AMBER
 ERROR no map function for S CYS :data= 221 CYS S 2001 Zn Zn 2.13

I saw that some people recommended to use the "raw" sander foramt. Could any one give me some
examples how should I use it. I am beginner in AMber9.

Any help would be greatly appreciated.

Urszula Uciechowska

   Cenk Andac, M.S., Ph.D. Student
 School of Pharmacy at
 Gazi University-Ankara Turkiye
  Address: Bandirma Sok. No:6
 Etiler, Ankara, 06330 Turkey
 Cell: +90-(536)-4813012

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