[MMTK] Conjugate gradient minimization in 2.2b6
Berit Hinnemann
Berit.Hinnemann@fysik.dtu.dk
Fri, 17 Aug 2001 10:46:25 +0200
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Hi all,
I am trying to do conjugate gradient minimization with fixed atoms, now
with the beta version of MMTK, 2.2b6, and I encounter the same problems
as I described in an earlier email.
I am using the script "chain_allCH3.py" and the input file "gly.pdb"
attached to the email. This is a simulation of two small glycine chains
terminated with "ace_beginning_nt" and "nmethyl_ct". I keep the four
C-atoms of the end methyl groups (CH3) fixed. Comparing the output file
"gly_allCH3_end.pdb" of the end configuration with the input file one
can see that only the first atom "unverse.proteins[0][0].CH3" has been
kept fixed. The positions of the other CH3 atoms have changed.
I have tried to keep different atoms fixed. The only atom which is kept
fixed is "unverse.proteins[0][0].CH3", all other atoms or combinations
of them change their positions even though their attribute "fixed" is
set to one. Another observation is that when I try to keep different
sets of atoms fixed, I get a different end configuration each time, just
that the atoms with atribute "fixed" set to one also change their
positions.
Has anybody encountered the same problems in the beta version?
Thanks,
Berit
--
Berit Hinnemann
Center for Atomic-Scale Materials Physics (CAMP)
Dept. of Physics, Technical University of Denmark
Building 307, DK-2800 Lyngby, Denmark
Phone: +45 4525 3209, Fax: +45 4593 2399
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from MMTK import *
from MMTK.Proteins import PeptideChain, Protein
from MMTK.ForceFields import Amber94ForceField
from MMTK.Minimization import ConjugateGradientMinimizer
from MMTK.Visualization import view
from MMTK.PDB import PDBConfiguration, PDBOutputFile
from MMTK.Trajectory import Trajectory, TrajectoryOutput, LogOutput, StandardLogOutput
from MMTK.DCD import writeDCDPDB
universe = InfiniteUniverse(Amber94ForceField())
conf = PDBConfiguration('gly.pdb')
#Change that for other output file names
fil = 'gly_allCH3'
chains = map(PeptideChain, conf.peptide_chains)
universe.proteins = Protein(chains)
outfile = PDBOutputFile('gly_control.pdb')
outfile.write(universe.proteins)
outfile.close()
trajectory = Trajectory(universe, fil+".nc", "w", "CG on chain")
#Fix the end-carbon atoms
upr = universe.proteins
upr[0][0].CH3.fixed = 1
upr[0][-1].CH3.fixed = 1
upr[1][0].CH3.fixed = 1
upr[1][-1].CH3.fixed = 1
# Minimize
minimizer = ConjugateGradientMinimizer(universe,
actions=[TrajectoryOutput(trajectory, ("energy",
"configuration"),0, None, 20),
StandardLogOutput(10),
LogOutput(fil+'.log', first=0, last=None, skip=10)])
minimizer(convergence = 1.e-3, steps = 10000)
writeDCDPDB(trajectory.configuration, fil+'.dcd', fil+'.pdb')
outfile2 = PDBOutputFile(fil+'_end.pdb')
outfile2.write(universe.proteins)
trajectory.close()
view(universe)
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ATOM 1 CH3 ACE A 1 14.295 4.506 3.955 0.00 0.00 C
ATOM 2 HH31 ACE A 1 14.051 3.600 4.551 0.00 0.00 H
ATOM 3 HH32 ACE A 1 14.887 4.213 3.063 0.00 0.00 H
ATOM 4 HH33 ACE A 1 14.887 5.209 4.578 0.00 0.00 H
ATOM 5 C ACE A 1 13.033 5.169 3.520 0.00 0.00 C
ATOM 6 O ACE A 1 13.059 6.196 2.844 0.00 0.00 O
ATOM 7 N GLY A 2 11.836 4.445 3.325 0.00 0.00 N
ATOM 8 O GLY A 2 9.588 3.012 3.087 0.00 0.00 O
ATOM 9 HA GLY A 2 10.585 6.065 2.883 0.00 0.00 H
ATOM 10 CA GLY A 2 10.604 5.169 3.520 0.00 0.00 C
ATOM 11 H GLY A 2 11.747 3.430 3.239 0.00 0.00 H
ATOM 12 C GLY A 2 9.429 4.244 3.210 0.00 0.00 C
ATOM 13 3HA GLY A 2 10.507 5.525 4.561 0.00 0.00 H
ATOM 14 N GLY A 3 8.233 4.851 3.109 0.00 0.00 N
ATOM 15 O GLY A 3 5.996 6.286 3.348 0.00 0.00 O
ATOM 16 HA GLY A 3 6.973 3.231 3.560 0.00 0.00 H
ATOM 17 CA GLY A 3 7.001 4.123 2.922 0.00 0.00 C
ATOM 18 H GLY A 3 8.119 5.860 3.225 0.00 0.00 H
ATOM 19 C GLY A 3 5.834 5.057 3.226 0.00 0.00 C
ATOM 20 3HA GLY A 3 6.906 3.759 1.884 0.00 0.00 H
ATOM 21 N NME A 4 4.682 4.364 3.226 0.00 0.00 N
ATOM 22 H NME A 4 4.646 3.368 3.226 0.00 0.00 H
ATOM 23 CH3 NME A 4 3.430 5.057 3.226 0.00 0.00 C
ATOM 24 HH31 NME A 4 3.360 5.695 2.319 0.00 0.00 H
ATOM 25 HH32 NME A 4 2.598 4.321 3.226 0.00 0.00 H
ATOM 26 HH33 NME A 4 3.360 5.695 4.133 0.00 0.00 H
TER 27 NME A 4
ATOM 28 CH3 ACE B 1 14.290 -0.826 3.956 0.00 0.00 C
ATOM 29 HH31 ACE B 1 14.046 -1.732 4.552 0.00 0.00 H
ATOM 30 HH32 ACE B 1 14.882 -1.119 3.064 0.00 0.00 H
ATOM 31 HH33 ACE B 1 14.882 -0.123 4.579 0.00 0.00 H
ATOM 32 C ACE B 1 13.028 -0.163 3.521 0.00 0.00 C
ATOM 33 O ACE B 1 13.054 0.864 2.845 0.00 0.00 O
ATOM 34 N GLY B 2 11.830 -0.893 3.342 0.00 0.00 N
ATOM 35 O GLY B 2 9.597 -2.329 3.113 0.00 0.00 O
ATOM 36 HA GLY B 2 10.570 0.720 2.871 0.00 0.00 H
ATOM 37 CA GLY B 2 10.599 -0.163 3.521 0.00 0.00 C
ATOM 38 H GLY B 2 11.716 -1.903 3.234 0.00 0.00 H
ATOM 39 C GLY B 2 9.433 -1.101 3.231 0.00 0.00 C
ATOM 40 3HA GLY B 2 10.506 0.215 4.554 0.00 0.00 H
ATOM 41 N GLY B 3 8.233 -0.491 3.140 0.00 0.00 N
ATOM 42 O GLY B 3 5.984 0.946 3.352 0.00 0.00 O
ATOM 43 HA GLY B 3 6.977 -2.102 3.601 0.00 0.00 H
ATOM 44 CA GLY B 3 7.002 -1.216 2.949 0.00 0.00 C
ATOM 45 H GLY B 3 8.145 0.525 3.217 0.00 0.00 H
ATOM 46 C GLY B 3 5.827 -0.287 3.241 0.00 0.00 C
ATOM 47 3HA GLY B 3 6.910 -1.589 1.913 0.00 0.00 H
ATOM 48 N NME B 4 4.675 -0.980 3.241 0.00 0.00 N
ATOM 49 H NME B 4 4.639 -1.976 3.241 0.00 0.00 H
ATOM 50 CH3 NME B 4 3.423 -0.287 3.241 0.00 0.00 C
ATOM 51 HH31 NME B 4 3.353 0.351 2.334 0.00 0.00 H
ATOM 52 HH32 NME B 4 2.591 -1.023 3.241 0.00 0.00 H
ATOM 53 HH33 NME B 4 3.353 0.351 4.148 0.00 0.00 H
TER 54 NME B 4
END
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ATOM 1 O ACE A 1 12.740 6.303 3.975 0.00 0.00 chai O
ATOM 2 1HH3 ACE A 1 14.032 3.594 4.487 0.00 0.00 chai H
ATOM 3 CH3 ACE A 1 14.295 4.506 3.955 0.00 0.00 chai C
ATOM 4 C ACE A 1 13.030 5.205 3.517 0.00 0.00 chai C
ATOM 5 2HH3 ACE A 1 14.897 4.267 3.080 0.00 0.00 chai H
ATOM 6 3HH3 ACE A 1 14.853 5.168 4.615 0.00 0.00 chai H
ATOM 7 N GLY A 2 12.286 4.571 2.614 0.00 0.00 chai N
ATOM 8 O GLY A 2 9.974 4.122 4.120 0.00 0.00 chai O
ATOM 9 HA GLY A 2 10.778 4.594 1.168 0.00 0.00 chai H
ATOM 10 CA GLY A 2 10.990 5.060 2.131 0.00 0.00 chai C
ATOM 11 H GLY A 2 12.625 3.665 2.307 0.00 0.00 chai H
ATOM 12 C GLY A 2 9.819 4.766 3.081 0.00 0.00 chai C
ATOM 13 3HA GLY A 2 11.047 6.139 1.984 0.00 0.00 chai H
ATOM 14 N GLY A 3 8.601 5.066 2.626 0.00 0.00 chai N
ATOM 15 O GLY A 3 6.305 5.054 1.138 0.00 0.00 chai O
ATOM 16 HA GLY A 3 7.081 5.308 4.049 0.00 0.00 chai H
ATOM 17 CA GLY A 3 7.353 4.618 3.251 0.00 0.00 chai C
ATOM 18 H GLY A 3 8.506 5.526 1.731 0.00 0.00 chai H
ATOM 19 C GLY A 3 6.195 4.544 2.252 0.00 0.00 chai C
ATOM 20 3HA GLY A 3 7.499 3.629 3.681 0.00 0.00 chai H
ATOM 21 N NME A 4 5.082 3.926 2.660 0.00 0.00 chai N
ATOM 22 3HH3 NME A 4 3.439 4.755 1.654 0.00 0.00 chai H
ATOM 23 1HH3 NME A 4 4.124 3.304 0.899 0.00 0.00 chai H
ATOM 24 CH3 NME A 4 3.875 3.774 1.852 0.00 0.00 chai C
ATOM 25 H NME A 4 5.118 3.471 3.568 0.00 0.00 chai H
ATOM 26 2HH3 NME A 4 3.147 3.156 2.380 0.00 0.00 chai H
TER 27 NME A 4
ATOM 28 O ACE B 1 13.257 1.888 1.932 0.00 0.00 chai O
ATOM 29 1HH3 ACE B 1 14.106 -1.061 2.191 0.00 0.00 chai H
ATOM 30 CH3 ACE B 1 13.686 -0.399 1.437 0.00 0.00 chai C
ATOM 31 C ACE B 1 12.930 0.720 2.114 0.00 0.00 chai C
ATOM 32 2HH3 ACE B 1 13.010 -0.948 0.783 0.00 0.00 chai H
ATOM 33 3HH3 ACE B 1 14.492 0.030 0.843 0.00 0.00 chai H
ATOM 34 N GLY B 2 11.905 0.370 2.886 0.00 0.00 chai N
ATOM 35 O GLY B 2 9.516 -0.434 4.069 0.00 0.00 chai O
ATOM 36 HA GLY B 2 10.701 2.063 2.855 0.00 0.00 chai H
ATOM 37 CA GLY B 2 11.066 1.343 3.586 0.00 0.00 chai C
ATOM 38 H GLY B 2 11.659 -0.605 2.974 0.00 0.00 chai H
ATOM 39 C GLY B 2 9.851 0.731 4.284 0.00 0.00 chai C
ATOM 40 3HA GLY B 2 11.666 1.873 4.325 0.00 0.00 chai H
ATOM 41 N GLY B 3 9.104 1.564 5.011 0.00 0.00 chai N
ATOM 42 O GLY B 3 5.760 2.065 4.777 0.00 0.00 chai O
ATOM 43 HA GLY B 3 7.617 1.953 6.435 0.00 0.00 chai H
ATOM 44 CA GLY B 3 7.827 1.226 5.651 0.00 0.00 chai C
ATOM 45 H GLY B 3 9.414 2.533 5.032 0.00 0.00 chai H
ATOM 46 C GLY B 3 6.651 1.224 4.669 0.00 0.00 chai C
ATOM 47 3HA GLY B 3 7.897 0.239 6.111 0.00 0.00 chai H
ATOM 48 N NME B 4 6.725 0.386 3.630 0.00 0.00 chai N
ATOM 49 3HH3 NME B 4 5.907 -0.605 1.968 0.00 0.00 chai H
ATOM 50 1HH3 NME B 4 4.743 0.329 2.935 0.00 0.00 chai H
ATOM 51 CH3 NME B 4 5.760 0.315 2.536 0.00 0.00 chai C
ATOM 52 H NME B 4 7.546 -0.212 3.611 0.00 0.00 chai H
ATOM 53 2HH3 NME B 4 5.889 1.171 1.871 0.00 0.00 chai H
TER 54 NME B 4
END
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