Hi amber users,
I want to simulate a catenan. In the first instance I created a mol2
file using antechamber. I submitted it to leap and managed to get the
topology and coordinate files for both vacuum form and solvated
molecule. However if I check the pdb file of the solvated molecule I
notice that the molecule was split. The first ring is labelled
correctly but the second ring is split in trio (like water) and the
last 100 water molecules are treated as one single molecule. To be
more specific it looks like this:
TOM 76 O23 DDD 1 22.267 28.626 19.731
ATOM 77 C37 DDD 1 21.319 25.320 18.077
ATOM 78 S3 DDD 1 20.677 26.058 16.533
ATOM 79 2H2 DDD 1 20.356 26.876 19.223
ATOM 80 3H2 DDD 1 20.639 24.494 18.390
ATOM 81 H24 DDD 1 22.327 24.874 17.921
ATOM 82 N4 DDD 1 23.078 22.362 15.073
ATOM 83 C38 DDD 1 22.646 23.158 13.940
ATOM 84 C39 DDD 1 22.216 24.571 14.380
ATOM 85 S4 DDD 1 20.624 24.477 15.268
ATOM 86 C40 DDD 1 23.823 23.248 12.996
ATOM 87 O12 DDD 1 23.593 23.548 11.689
ATOM 88 O24 DDD 1 25.050 23.556 13.502
ATOM 89 H25 DDD 1 21.826 22.652 13.377
ATOM 90 H26 DDD 1 23.966 22.563 15.541
ATOM 91 H27 DDD 1 22.086 25.228 13.488
ATOM 92 H28 DDD 1 23.018 25.020 15.011
TER
ATOM 93 C41 DDD 1 22.229 22.043 20.336
ATOM 94 C42 DDD 1 23.522 21.829 20.605
ATOM 95 C43 DDD 1 23.865 21.226 21.754
TER
ATOM 96 C44 DDD 1 22.937 20.829 22.651
ATOM 97 C45 DDD 1 21.627 21.028 22.368
ATOM 98 C46 DDD 1 21.295 21.641 21.212
TER
ATOM 99 C47 DDD 1 23.276 20.235 23.814
ATOM 100 C48 DDD 1 22.337 19.834 24.687
ATOM 101 C49 DDD 1 21.041 20.026 24.406
TER
[..........]
TER
ATOM 5919 H1 WAT 1913 16.782 17.863 5.164
ATOM 5920 H2 WAT 1913 15.298 18.026 4.916
ATOM 5921 O WAT 1914 26.554 28.651 6.156
TER
ATOM 5922 H1 WAT 1914 27.098 29.264 5.661
ATOM 5923 H2 WAT 1914 25.973 29.209 6.672
ATOM 5924 O WAT 1915 19.263 15.464 2.739
TER
ATOM 5925 H1 WAT 1915 19.787 15.710 3.501
ATOM 5926 H2 WAT 1915 19.045 16.296 2.319
ATOM 5927 O WAT 1916 22.356 17.606 -1.221
TER
ATOM 5928 H1 WAT 1916 22.098 18.528 -1.222
ATOM 5929 H2 WAT 1916 21.825 17.209 -0.531
ATOM 5930 O WAT 1917 13.119 22.722 -0.375
ATOM 5931 H1 WAT 1917 12.574 23.498 -0.243
ATOM 5932 H2 WAT 1917 13.997 23.069 -0.534
ATOM 5933 O WAT 1918 13.905 21.849 2.518
ATOM 5934 H1 WAT 1918 13.163 21.998 3.104
ATOM 5935 H2 WAT 1918 13.585 22.110 1.654
ATOM 5936 O WAT 1919 21.850 31.391 2.316
ATOM 5937 H1 WAT 1919 22.158 31.146 3.188
ATOM 5938 H2 WAT 1919 22.647 31.596 1.827
ATOM 5939 O WAT 1920 19.392 17.567 6.212
ATOM 5940 H1 WAT 1920 19.440 18.443 5.829
ATOM 5941 H2 WAT 1920 19.934 17.024 5.639
ATOM 5942 O WAT 1921 29.877 28.111 5.492
ATOM 5943 H1 WAT 1921 29.087 28.093 4.952
and so on...
Should I worry about that?
Now I still tried to minimize the structure and everything seemed to
work out fine. However when I tried to heat the system putting
restraints on the molecule DDD, I get the error of "segmentation
fault". I've checked and this is not a problem of cluster memory since
other simulation (much larger in size) are running fine.
Is this due to the fact that sander sees only part of the molecule and
the rest in a "trio" format? Is there any other way to simulate the
catenan? Shall I create separate mol2 files for each ring
individually ? If so, how do I "link" them in leap since there is no
physical /covalent connection between them?
Thanks,
Cristina
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Received on Sun Mar 08 2009 - 01:08:10 PST
