If your goal is to use the same rk2 and rk3 for all of your restraints, then
your restraint file is just fine. If rk2 and rk3 are specified in the first
restraint, then should rk2 and rk3 not be specified in the second restraint,
their values are assigned to be equal to the values of rk2 and rk3 in the
first restraint, and so on for subsequent restraints. If you want a
different rk2 and rk3 for each of your 6 distance restraints, then you
should specify rk2 and rk3 each. These can be written by hand in the
restraint file in the manner that they're written for the first restraint if
you're having trouble figuring out how to use makeDIST_RST to accomplish
this.
--Matthew Seetin
University of Rochester Medical Center
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf
Of qiaoyan
Sent: Tuesday, May 25, 2010 10:58 PM
To: AMBER
Subject: [AMBER] distance restraint
Dear amber uses:
I want to restrain 6 bond length, and I used makeDIST_RST to generate
the RST.dist file, but in the RST.dist file, rk2 and rk3 only appeared in
the first restraint, When I check the outfile, Number of restraints read =
6 ,is there any question about this problem?
RST.dist
#
# 19 GLN HE21 213 RES O8 2.5
&rst
ixpk= 0, nxpk= 0, iat= 313,3263, r1= 1.30, r2= 1.80, r3= 2.50, r4= 3.00,
rk2=0.0, rk3=20.0, ir6=1, ialtd=0,
&end
#
# 25 CYM HN 213 RES O8 2.5
&rst
ixpk= 0, nxpk= 0, iat= 364,3263, r1= 1.30, r2= 1.80, r3= 2.50, r4= 3.00,
&end
#
# 25 CYM SG 213 RES C7 4.0
&rst
ixpk= 0, nxpk= 0, iat= 370,3262, r1= 1.30, r2= 1.80, r3= 4.00, r4= 4.50,
&end
#
# 159 HIP HND 213 RES N9 3.5
&rst
ixpk= 0, nxpk= 0, iat=2442,3260, r1= 1.30, r2= 1.80, r3= 3.50, r4= 4.00,
&end
#
# 66 GLY HN 213 RES O4 2.5
&rst
ixpk= 0, nxpk= 0, iat= 991,3270, r1= 1.30, r2= 1.80, r3= 2.50, r4= 3.00,
&end
#
# 66 GLY O 213 RES H29 2.5
&rst
ixpk= 0, nxpk= 0, iat= 996,3279, r1= 1.30, r2= 1.80, r3= 2.50, r4= 3.00,
&end
2010-05-26
qiaoyan
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 25 2010 - 22:00:04 PDT
