Slowcool problems with covalently-bound ligand
Kristin Fox
foxk at UNION.EDU
Fri Aug 21 10:41:49 EST 1998
I am refining a structure which has a covalently bound ligand. I have
prepared parameter and topology files using XPLO2D for a new aa residue
which is the normal residue plus the ligand atoms. After using XPLO2D, I
edited the parameter and topology files to ensure that the atom types for
the main chain and side chain atoms were consistent with toph19.pep so
that peptide bonds would be formed as usual.
All is seemingly OK through generate, check and prepstage. The PDB file
output after prepstage looks fine. (The only sign of a problem is a high
weight from check, approx. 5 times the normal for this structure under the
same conditions.)
In slowcool, problems develop, it never blows up, but
1. The R-factors never get up into the high thirties (like they usually
do) when the temp=3000K.
2. The run never cools down, but stays up around an average of 2800
degrees over many, many cycles. There is also a large fluctuation in the
temperature of the slowcool. (see data below)
Has anybody ever seen this before? It seems that something is wrong with
the parameter and/or topology files I have created, but I am not sure what
to look for as the source of the problem.
Thanks,
Kristin
Kristin M. Fox
Assistant Professor of Chemistry
Union College
Schenectady, NY 12308
foxk at union.edu
| E(kin)+E(total)=68367.128 E(kin)=17409.272
temperature=2462.267 |
| E(kin)+E(total)=66237.543 E(kin)=14917.434
temperature=2109.835 |
| E(kin)+E(total)=74686.218 E(kin)=25065.025
temperature=3545.052 |
| E(kin)+E(total)=70852.479 E(kin)=17975.234
temperature=2542.313 |
| E(kin)+E(total)=69358.841 E(kin)=17038.663
temperature=2409.850 |
| E(kin)+E(total)=68675.869 E(kin)=15249.382
temperature=2156.784 |
| E(kin)+E(total)=68098.466 E(kin)=16957.068
temperature=2398.309 |
| E(kin)+E(total)=68255.314 E(kin)=22255.306
temperature=3147.661 |
| E(kin)+E(total)=68254.800 E(kin)=22254.792
temperature=3147.589 |
| E(kin)+E(total)=89787.843 E(kin)=23788.925
temperature=3364.568 |
| E(kin)+E(total)=84961.673 E(kin)=23806.110
temperature=3366.998 |
| E(kin)+E(total)=77549.933 E(kin)=24442.756
temperature=3457.042 |
| E(kin)+E(total)=74612.227 E(kin)=16896.398
temperature=2389.729 |
| E(kin)+E(total)=73939.744 E(kin)=16476.902
temperature=2330.397 |
| E(kin)+E(total)=71811.486 E(kin)=20213.368
temperature=2858.862 |
| E(kin)+E(total)=70218.366 E(kin)=16056.700
temperature=2270.966 |
| E(kin)+E(total)=67923.067 E(kin)=14985.334
temperature=2119.439 |
| E(kin)+E(total)=68172.148 E(kin)=14614.049
temperature=2066.926 |
| E(kin)+E(total)=67107.614 E(kin)=19803.135
temperature=2800.841 |
| E(kin)+E(total)=67106.006 E(kin)=19801.526
temperature=2800.613 |
| E(kin)+E(total)=68850.773 E(kin)=18828.082
temperature=2662.935 |
| E(kin)+E(total)=66820.858 E(kin)=15576.020
temperature=2202.982 |
| E(kin)+E(total)=65857.717 E(kin)=14314.926
temperature=2024.620 |
| E(kin)+E(total)=64836.556 E(kin)=14704.080
temperature=2079.660 |
| E(kin)+E(total)=65943.706 E(kin)=13366.281
temperature=1890.449 |
| E(kin)+E(total)=65098.205 E(kin)=16783.835
temperature=2373.808 |
| E(kin)+E(total)=63621.166 E(kin)=17182.729
temperature=2430.225 |
| E(kin)+E(total)=63335.754 E(kin)=11180.484
temperature=1581.303 |
| E(kin)+E(total)=63761.615 E(kin)=14938.874
temperature=2112.868 |
| E(kin)+E(total)=63154.799 E(kin)=17178.730
temperature=2429.660 |
| E(kin)+E(total)=63152.867 E(kin)=17176.798
temperature=2429.387 |
| E(kin)+E(total)=62690.647 E(kin)=14871.919
temperature=2103.398 |
| E(kin)+E(total)=62452.988 E(kin)=13620.873
temperature=1926.457 |
| E(kin)+E(total)=63003.512 E(kin)=13790.148
temperature=1950.399 |
| E(kin)+E(total)=62727.841 E(kin)=13197.911
temperature=1866.636 |
| E(kin)+E(total)=66301.496 E(kin)=17676.927
temperature=2500.122 |
| E(kin)+E(total)=65591.139 E(kin)=17889.419
temperature=2530.176 |
| E(kin)+E(total)=64436.297 E(kin)=17180.213
temperature=2429.870 |
| E(kin)+E(total)=63698.978 E(kin)=13563.704
temperature=1918.372 |
| E(kin)+E(total)=67829.622 E(kin)=14447.986
temperature=2043.439 |
| E(kin)+E(total)=66141.762 E(kin)=16953.352
temperature=2397.784 |
| E(kin)+E(total)=66140.790 E(kin)=16952.380
temperature=2397.646 |
| E(kin)+E(total)=66667.645 E(kin)=12073.973
temperature=1707.673 |
| E(kin)+E(total)=66658.364 E(kin)=18539.704
temperature=2622.148 |
| E(kin)+E(total)=63609.760 E(kin)=16247.533
temperature=2297.957 |
| E(kin)+E(total)=67558.115 E(kin)=16083.725
temperature=2274.789 |
| E(kin)+E(total)=66341.763 E(kin)=18555.479
temperature=2624.379 |
| E(kin)+E(total)=65023.719 E(kin)=16137.486
temperature=2282.392 |
| E(kin)+E(total)=63029.733 E(kin)=17337.660
temperature=2452.138 |
| E(kin)+E(total)=62587.274 E(kin)=13996.834
temperature=1979.631 |
| E(kin)+E(total)=62529.057 E(kin)=13534.321
temperature=1914.216 |
| E(kin)+E(total)=62602.159 E(kin)=14762.613
temperature=2087.938 |
| E(kin)+E(total)=62600.860 E(kin)=14761.314
temperature=2087.755 |
| E(kin)+E(total)=62270.395 E(kin)=11924.942
temperature=1686.595 |
| E(kin)+E(total)=62982.983 E(kin)=13972.712
temperature=1976.219 |
| E(kin)+E(total)=62404.388 E(kin)=16041.270
temperature=2268.784 |
| E(kin)+E(total)=63021.834 E(kin)=18147.599
temperature=2566.691 |
| E(kin)+E(total)=62774.272 E(kin)=13901.512
temperature=1966.149 |
| E(kin)+E(total)=66069.937 E(kin)=16895.603
temperature=2389.616 |
| E(kin)+E(total)=65434.677 E(kin)=14456.145
temperature=2044.593 |
| E(kin)+E(total)=65627.313 E(kin)=14079.196
temperature=1991.280 |
| E(kin)+E(total)=66321.977 E(kin)=16671.485
temperature=2357.918 |
| E(kin)+E(total)=65615.382 E(kin)=15649.040
temperature=2213.309 |
| E(kin)+E(total)=65614.085 E(kin)=15647.743
temperature=2213.126 |
| E(kin)+E(total)=64947.165 E(kin)=14115.953
temperature=1996.479 |
| E(kin)+E(total)=63972.899 E(kin)=14981.092
temperature=2118.839 |
| E(kin)+E(total)=63271.234 E(kin)=16686.720
temperature=2360.073 |
| E(kin)+E(total)=61788.253 E(kin)=15395.838
temperature=2177.498 |
| E(kin)+E(total)=61440.760 E(kin)=13907.166
temperature=1966.949 |
| E(kin)+E(total)=61862.152 E(kin)=13997.541
temperature=1979.731 |
| E(kin)+E(total)=61692.038 E(kin)=16806.190
temperature=2376.970 |
| E(kin)+E(total)=61237.294 E(kin)=12585.856
temperature=1780.070 |
| E(kin)+E(total)=61131.267 E(kin)=12855.444
temperature=1818.199 |
| E(kin)+E(total)=61765.602 E(kin)=13959.630
temperature=1974.369 |
| E(kin)+E(total)=61759.517 E(kin)=13953.544
temperature=1973.508 |
| E(kin)+E(total)=61251.931 E(kin)=13542.291
temperature=1915.343 |
| E(kin)+E(total)=60985.282 E(kin)=14898.877
temperature=2107.211 |
| E(kin)+E(total)=60649.654 E(kin)=13525.417
temperature=1912.957 |
| E(kin)+E(total)=60549.207 E(kin)=13830.673
temperature=1956.130 |
| E(kin)+E(total)=60532.956 E(kin)=12330.679
temperature=1743.980 |
| E(kin)+E(total)=60469.497 E(kin)=12341.523
temperature=1745.513 |
| E(kin)+E(total)=61587.478 E(kin)=15460.415
temperature=2186.631 |
| E(kin)+E(total)=60842.708 E(kin)=13697.632
temperature=1937.314 |
| E(kin)+E(total)=80446.907 E(kin)=22344.683
temperature=3160.302 |
| E(kin)+E(total)=77601.337 E(kin)=20697.146
temperature=2927.284 |
| E(kin)+E(total)=77600.103 E(kin)=20695.913
temperature=2927.110 |
| E(kin)+E(total)=82720.189 E(kin)=17135.498
temperature=2423.546 |
| E(kin)+E(total)=94465.430 E(kin)=25646.127
temperature=3627.240 |
| E(kin)+E(total)=89308.450 E(kin)=24095.448
temperature=3407.920 |
| E(kin)+E(total)=75759.275 E(kin)=26436.192
temperature=3738.982 |
| E(kin)+E(total)=155457.143 E(kin)=89196.637
temperature=12615.455 |
| E(kin)+E(total)=137223.887 E(kin)=23012.918
temperature=3254.814 |
| E(kin)+E(total)=125147.367 E(kin)=43300.960
temperature=6124.237 |
| E(kin)+E(total)=114764.182 E(kin)=38935.532
temperature=5506.816 |
| E(kin)+E(total)=104411.916 E(kin)=31258.226
temperature=4420.982 |
| E(kin)+E(total)=92787.488 E(kin)=32801.441
temperature=4639.246 |
| E(kin)+E(total)=92786.687 E(kin)=32800.639
temperature=4639.132 |
| E(kin)+E(total)=89919.881 E(kin)=14942.108
temperature=2113.325 |
| E(kin)+E(total)=87389.907 E(kin)=22213.599
temperature=3141.763 |
| E(kin)+E(total)=82155.033 E(kin)=26471.659
temperature=3743.998 |
| E(kin)+E(total)=77790.882 E(kin)=19100.145
temperature=2701.414 |
| E(kin)+E(total)=75200.661 E(kin)=18551.262
temperature=2623.783 |
| E(kin)+E(total)=69087.160 E(kin)=15664.524
temperature=2215.499 |
| E(kin)+E(total)=66932.927 E(kin)=23274.159
temperature=3291.762 |
| E(kin)+E(total)=75039.158 E(kin)=15140.952
temperature=2141.448 |
| E(kin)+E(total)=74598.984 E(kin)=17868.826
temperature=2527.263 |
| E(kin)+E(total)=72356.596 E(kin)=13896.995
temperature=1965.510 |
| E(kin)+E(total)=72355.032 E(kin)=13895.431
temperature=1965.289 |
| E(kin)+E(total)=72970.493 E(kin)=14877.488
temperature=2104.186 |
| E(kin)+E(total)=72014.117 E(kin)=14850.058
temperature=2100.306 |
| E(kin)+E(total)=80825.259 E(kin)=22917.010
temperature=3241.249 |
| E(kin)+E(total)=118571.024 E(kin)=27246.159
temperature=3853.539 |
| E(kin)+E(total)=114579.645 E(kin)=23929.867
temperature=3384.502 |
| E(kin)+E(total)=117154.553 E(kin)=42253.803
temperature=5976.133 |
| E(kin)+E(total)=104033.139 E(kin)=21803.315
temperature=3083.734 |
| E(kin)+E(total)=107569.754 E(kin)=37064.403
temperature=5242.174 |
| E(kin)+E(total)=98327.179 E(kin)=25974.034
temperature=3673.617 |
| E(kin)+E(total)=92478.164 E(kin)=23950.200
temperature=3387.377 |
| E(kin)+E(total)=92477.905 E(kin)=23949.942
temperature=3387.341 |
| E(kin)+E(total)=99511.377 E(kin)=15087.922
temperature=2133.948 |
| E(kin)+E(total)=95712.024 E(kin)=22782.409
temperature=3222.212 |
| E(kin)+E(total)=91819.045 E(kin)=16034.778
temperature=2267.866 |
| E(kin)+E(total)=89921.331 E(kin)=19352.693
temperature=2737.133 |
| E(kin)+E(total)=87746.848 E(kin)=16807.755
temperature=2377.191 |
| E(kin)+E(total)=93538.596 E(kin)=25742.746
temperature=3640.905 |
| E(kin)+E(total)=92924.032 E(kin)=16506.660
temperature=2334.606 |
| E(kin)+E(total)=89272.881 E(kin)=19439.910
temperature=2749.468 |
| E(kin)+E(total)=96273.834 E(kin)=27494.783
temperature=3888.703 |
| E(kin)+E(total)=90320.139 E(kin)=15252.198
temperature=2157.182 |
| E(kin)+E(total)=90319.867 E(kin)=15251.926
temperature=2157.144 |
| E(kin)+E(total)=89691.282 E(kin)=23676.255
temperature=3348.632 |
| E(kin)+E(total)=83427.840 E(kin)=19657.584
temperature=2780.255 |
| E(kin)+E(total)=76673.753 E(kin)=14551.102
temperature=2058.023 |
| E(kin)+E(total)=80415.628 E(kin)=14179.520
temperature=2005.469 |
| E(kin)+E(total)=81245.688 E(kin)=13365.098
temperature=1890.282 |
| E(kin)+E(total)=80703.106 E(kin)=15916.119
temperature=2251.084 |
| E(kin)+E(total)=88271.841 E(kin)=17973.009
temperature=2541.998 |
| E(kin)+E(total)=98974.516 E(kin)=20560.602
temperature=2907.972 |
| E(kin)+E(total)=92931.660 E(kin)=27773.117
temperature=3928.069 |
| E(kin)+E(total)=101146.112 E(kin)=21499.315
temperature=3040.738 |
| E(kin)+E(total)=101145.305 E(kin)=21498.508
temperature=3040.624 |
| E(kin)+E(total)=96160.900 E(kin)=21007.642
temperature=2971.199 |
Kristin M. Fox
Assistant Professor
Department of Chemistry
Union College
foxk at union.edu
(518)388-6250** on sabbatical 6/98-12/98 phone (518) 486-9154
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