David (or anyone who can help),
I'm trying to fix torsion angles using torsion restraints
in an NMR restraint file.
FROM THE RESTRAINT FILE:
#####################################
# C6-C7-N1-C8
&rst
rk2=10000.0, rk3=10000.0, ialtd=0,
iat=2273,2274,2263,2275, r1=-180.10, r2=-180.05, r3=-179.95, r4=-179.90, /
#####################################
When I look at the output file, it appears that the penalty
for the torsion angle restraints is being calculated differently
from the NOE-distance penalties, even though IPNLTY is set to 1.
FROM THE OUTPUT FILE:
####################################
Restraints, deviations, and energy contributions: pencut = 0.00
------------------------------------------------------------------------------
First atom Last atom curr. value target deviation penalty
------------------------------------------------------------------------------
C7 cap 146 -- N1 cap 146: -180.156 -180.050 0.106 0.025 t
N1 cap 146 -- C8 cap 146: -180.078 -180.050 0.028 0.002 t
C8 cap 146 -- N2 cap 146: 180.292 180.050 0.242 0.066 t
HE1 HID 62 -- *HB3 ALA 64: 3.980 3.800 0.180 0.645 d 0: 0
HZ2 TRP 23 -- *H03 cap 146: 5.517 5.500 0.017 0.006 d 0: 0
HH2 TRP 23 -- *H03 cap 146: 5.401 5.500 0.000 0.000 d 0: 0
H6 cap 146 -- *HG13 VAL 27: 2.867 5.500 0.000 0.000 d 0: 0
*HG13 VAL 27 -- H5 cap 146: 5.161 5.500 0.000 0.000 d 0: 0
HB VAL 59 -- H6 cap 146: 2.710 5.500 0.000 0.000 d 0: 0
*HG23 VAL 59 -- H6 cap 146: 4.637 5.500 0.000 0.000 d 0: 0
*HB3 ALA 65 -- H6 cap 146: 5.472 5.500 0.000 0.000 d 0: 0
*HB3 ALA 65 -- H3 cap 146: 2.993 5.500 0.000 0.000 d 0: 0
*HB3 ALA 31 -- H5 cap 146: 3.091 3.800 0.000 0.000 d 0: 0
*HG23 ILE 141 -- *H03 cap 146: 4.239 4.300 0.000 0.000 d 0: 0
Total distance penalty: 0.650
Total torsion penalty: 0.093
------------------------------------------------------------------------------
#####################################
I assume it is the penalty that is used during the structure calculations.
If so, is there a flag or parameter that allows the penalty for torsion angles
to be calculated linearly with deviation, or better yet, to scale at a much
greater rate than linear? The torsion angles are varying significantly during
the calculations, and I'd like to keep them relatively rigid.
Thanks,
Mike
--
*********************************
Michael F. Summers
Department of Chemistry and Biochemistry
and Howard Hughes Medical Institute
University of Maryland Baltimore County
1000 Hilltop Circle
Baltimore, MD 21250
Phone: (410)-455-2527
FAX: (410)-455-1174
Email: summers.hhmi.umbc.edu
Web: www.hhmi.umbc.edu
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Received on Sun Jan 07 2007 - 06:07:08 PST
