[MMTK] Problems with constraints and conjugate gradient minimization
Berit Hinnemann
Berit.Hinnemann@fysik.dtu.dk
Mon, 06 Aug 2001 14:18:06 +0200
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Hi all,
I am trying to do a conjugate-gradient minimization of two small
parallel chains of glycine and would like to keep some atoms fixed in
the process. The chains are terminated with the groups
"ace_beginning_nt" and "nmethyl_ct" which are defined in the database
that comes with MMTK. I have attached the input file, "gly.pdb" to the
email.
For the minimization I am using the script at the bottom of the mail. I
keep the four methyl group atoms (CH3) at the end of the chain fixed by
setting an attribute "fixed" to one. When I now check the PDB file of
the chains after minimization, in my script "gly_allCH3_end.pdb", I find
that the atom 'upr[0][0].CH3' has indeed been kept fixed, but the
position of the other three have changed. The file "gly_allCH3_end.pdb"
is also attached to the mail.
I have tested this by trying to keep several combinations of atoms
fixed. The only atom which is actually kept fixed is 'upr[0][0].CH3'.
When I set the attribute "fixed" to one for any other atom or
combination of them, they are not kept fixed. Another thing, the
minimization always ends up at the same energy, no matter if I try to
keep atoms fixed or not.
Has anybody encountered the same problem and knows how to fix it? If
necessary, I can of course provide further output files I got or other
details.
Thanks a lot in advance,
Berit
--
Berit Hinnemann, Dipl.-Phys.
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
---Script for minimization-----------------------------------------
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')
chains = map(PeptideChain, conf.peptide_chains)
universe.proteins = Protein(chains)
outfile = PDBOutputFile('gly_control.pdb')
outfile.write(universe.proteins)
outfile.close()
trajectory = Trajectory(universe, "gly_allCH3.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('gly_allCH3.log', first=0, last=None, skip=10)])
minimizer(convergence = 1.e-3, steps = 10000)
writeDCDPDB(trajectory.configuration, 'gly_allCH3.dcd',
'gly_allCH3.pdb')
outfile2 = PDBOutputFile('gly_allCH3_end.pdb')
outfile2.write(universe.proteins)
trajectory.close()
view(universe)
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name="gly.pdb"
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Content-Disposition: inline;
filename="gly.pdb"
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 12.828 6.269 4.571 0.00 0.00 chai O
ATOM 2 1HH3 ACE A 1 14.003 3.488 4.204 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 13.053 5.350 3.794 0.00 0.00 chai C
ATOM 5 2HH3 ACE A 1 14.861 4.515 3.025 0.00 0.00 chai H
ATOM 6 3HH3 ACE A 1 14.901 4.921 4.758 0.00 0.00 chai H
ATOM 7 N GLY A 2 12.255 5.036 2.776 0.00 0.00 chai N
ATOM 8 O GLY A 2 9.918 4.087 4.010 0.00 0.00 chai O
ATOM 9 HA GLY A 2 10.832 5.745 1.423 0.00 0.00 chai H
ATOM 10 CA GLY A 2 10.961 5.670 2.502 0.00 0.00 chai C
ATOM 11 H GLY A 2 12.546 4.246 2.208 0.00 0.00 chai H
ATOM 12 C GLY A 2 9.775 4.894 3.089 0.00 0.00 chai C
ATOM 13 3HA GLY A 2 10.949 6.677 2.920 0.00 0.00 chai H
ATOM 14 N GLY A 3 8.586 5.083 2.517 0.00 0.00 chai N
ATOM 15 O GLY A 3 6.280 5.376 1.032 0.00 0.00 chai O
ATOM 16 HA GLY A 3 7.089 4.388 3.809 0.00 0.00 chai H
ATOM 17 CA GLY A 3 7.436 4.222 2.789 0.00 0.00 chai C
ATOM 18 H GLY A 3 8.481 5.754 1.768 0.00 0.00 chai H
ATOM 19 C GLY A 3 6.265 4.442 1.832 0.00 0.00 chai C
ATOM 20 3HA GLY A 3 7.754 3.185 2.692 0.00 0.00 chai H
ATOM 21 N NME A 4 5.255 3.573 1.927 0.00 0.00 chai N
ATOM 22 3HH3 NME A 4 3.522 4.554 1.268 0.00 0.00 chai H
ATOM 23 1HH3 NME A 4 4.316 3.536 0.052 0.00 0.00 chai H
ATOM 24 CH3 NME A 4 4.046 3.610 1.107 0.00 0.00 chai C
ATOM 25 H NME A 4 5.385 2.815 2.591 0.00 0.00 chai H
ATOM 26 2HH3 NME A 4 3.389 2.781 1.371 0.00 0.00 chai H
TER 27 NME A 4
ATOM 28 O ACE B 1 13.047 2.630 1.292 0.00 0.00 chai O
ATOM 29 1HH3 ACE B 1 14.141 -0.225 0.989 0.00 0.00 chai H
ATOM 30 CH3 ACE B 1 13.675 0.533 0.362 0.00 0.00 chai C
ATOM 31 C ACE B 1 12.811 1.429 1.217 0.00 0.00 chai C
ATOM 32 2HH3 ACE B 1 13.062 0.065 -0.406 0.00 0.00 chai H
ATOM 33 3HH3 ACE B 1 14.448 1.137 -0.111 0.00 0.00 chai H
ATOM 34 N GLY B 2 11.806 0.848 1.869 0.00 0.00 chai N
ATOM 35 O GLY B 2 9.828 -0.514 3.249 0.00 0.00 chai O
ATOM 36 HA GLY B 2 10.337 2.300 2.136 0.00 0.00 chai H
ATOM 37 CA GLY B 2 10.889 1.581 2.740 0.00 0.00 chai C
ATOM 38 H GLY B 2 11.658 -0.147 1.779 0.00 0.00 chai H
ATOM 39 C GLY B 2 9.878 0.696 3.470 0.00 0.00 chai C
ATOM 40 3HA GLY B 2 11.470 2.124 3.487 0.00 0.00 chai H
ATOM 41 N GLY B 3 9.073 1.306 4.342 0.00 0.00 chai N
ATOM 42 O GLY B 3 6.307 1.488 3.723 0.00 0.00 chai O
ATOM 43 HA GLY B 3 8.016 1.105 6.130 0.00 0.00 chai H
ATOM 44 CA GLY B 3 8.058 0.623 5.154 0.00 0.00 chai C
ATOM 45 H GLY B 3 9.197 2.310 4.442 0.00 0.00 chai H
ATOM 46 C GLY B 3 6.643 0.647 4.557 0.00 0.00 chai C
ATOM 47 3HA GLY B 3 8.354 -0.416 5.304 0.00 0.00 chai H
ATOM 48 N NME B 4 5.771 -0.231 5.067 0.00 0.00 chai N
ATOM 49 3HH3 NME B 4 3.854 0.604 4.871 0.00 0.00 chai H
ATOM 50 1HH3 NME B 4 4.311 -0.537 3.591 0.00 0.00 chai H
ATOM 51 CH3 NME B 4 4.370 -0.336 4.662 0.00 0.00 chai C
ATOM 52 H NME B 4 6.122 -0.878 5.757 0.00 0.00 chai H
ATOM 53 2HH3 NME B 4 3.879 -1.144 5.206 0.00 0.00 chai H
TER 54 NME B 4
END
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