Hi Charles and xplor users,
I am having trouble with the minimization script below which is based mostly
on python/tests/planeDistTest.py. I have a protein with several helical
segments and have positioned a phenylalanine (not connected to the protein)
about 20 ang. from one of the helix axes. This axis is very close to the
plane defined by the PHE ring. I have large helix to plane distances in the
restraint file (p.tbl) so the helix should move away from the plane. However
the output structures (protein and PHE) are exactly the same as the input
and I get the following:
First several lines like the following
%PARRDR-ERROR: duplication of nonbonded entry OH
%PARRDR-ERROR: duplication of nonbonded entry S
And then three sets of the following lines (one set for each minimization)
planeDist PLAN 1100 ANI OO PLAN 1100 ANI X PLAN 1100 ANI Y 5
torsionTopology: WARNING: oTensor containing PLAN 1100 ANI OO is not
specified
*-- POWELL ------ step= 0 --- stepsize= 0.01000 --- energy evals=
2 -*
| E(poten)= 0.0000000 grad= 0.0000000 planeDist=
0.0000000 |
*---------------------------------------------------------------------------
---*
Powell::step: normal exit.
*-- POWELL ------ step= 1 --- stepsize= 0.01000 --- energy evals=
0 -*
| E(poten)= 0.0000000 grad= 0.0000000 planeDist=
0.0000000 |
*---------------------------------------------------------------------------
---*
The output pdb file contains the following at the end
ATOM 2982 OO ANI 1100 144.370 -2.181 5.466 1.00 0.00 PLAN
ATOM 2983 X ANI 1100 144.370 -2.949 4.826 1.00 0.00 PLAN
ATOM 2984 Y ANI 1100 143.503 -1.861 5.082 1.00 0.00 PLAN
The following are the pdb lines for the atoms used to define the plane
ATOM 2973 CE1 PHE 200 144.633 18.078 22.537 1.00 0.00
ATOM 2977 CZ PHE 200 145.499 17.012 22.299 1.00 0.00
ATOM 2978 HZ PHE 200 145.266 16.295 21.527 1.00 0.00
What am I doing wrong?
Thanks,
Jeff Ellena
The python xplornih script follows
# plane distance orientation
import sys
sys.stderr = sys.stdout
from os import environ as env
xplor.parseArguments() # check for typos on the command-line
from ivm import IVM
from xplor import command
from planeDistTools import create_PlaneDistPot
write = sys.stdout.write
#! read in the PSF file and initial structure
#command("set mess=off echo=off end")
command("param @TOPPAR:protein.par end")
#command("set mess=off echo=off end")
import protocol
import psfGen
psfGen.pdbToPSF("dsbb.pdb")
psfGen.pdbToPSF("phe.pdb")
totStructs = 3
proc = int( env["XPLOR_PROCESS"] )
numProcs = int( env["XPLOR_NUM_PROCESSES"] )
start = (proc * totStructs) / numProcs
stop = ((proc+1) * totStructs) / numProcs
# Calculate how many structures per processor
for count in range(start,stop):
xplor.command("delete sele=(segid PLAN) end")
protocol.initCoords(files=["dsbb.pdb", "phe.pdb"],erase=True)
planePot = create_PlaneDistPot("planeDist",restraints="p.tbl",
oAtom="resid 200 and name CE1",
xAtom="resid 200 and name CZ",
yAtom="resid 200 and name HZ")
planePot.setFreedom('fix')
planePot.setScale(1000)
min=IVM()
import planeDistTools
planeDistTools.topologySetup(min,planePot)
protocol.torsionTopology( min )
protocol.initMinimize(min,
potList=[planePot],
numSteps=10000)
min.run()
command("write coor output=test5yy_%d.pdb end" % count)
pass
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