AMBER Archive (2007)

Subject: AMBER: torsion angle penalty calculation

From: Mike Summers (summers_at_hhmi.umbc.edu)
Date: Wed Jan 03 2007 - 09:18:34 CST


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_at_hhmi.umbc.edu Web: www.hhmi.umbc.edu ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu