Hi,
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.).
# DISTANCE RESTRAINT SECTION
# NOE restraint between protons HA and HB
# For instance their atom IDs (iat) are 18,42, respectively
&rst
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,
&end
#Additional NOE restraint(s) were added below in a similar format
#for distance restraints above
#
# TORSION RESTRAINT SECTION
# 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
&rst
iat = 19, 2, 1, 23,
r1 = 59, r2 = 60, r3 = 60, r4 = 61,
rk2 =3, rk3 =3,
&end
regards,
jenk
Urszula Uciechowska <urszula.uciechowska.pharmazie.uni-halle.de> 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
prot.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
E-Mail:cenk_andac.yahoo.com
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Received on Wed Oct 25 2006 - 06:07:23 PDT
