I am trying to verify chemical bonds commanded from leap with
---VMD
---parmed.py
---parm7 file
I assume that in parm7 file:
BONDS INC HYDROGEN
This section contains a list of every bond in the system in which at least
one atom is Hydrogen. Each bond is identified by 3 integers—the two
atoms involved in the bond and the index into the BOND FORCE CONSTANT
and BOND EQUIL VALUE. For run-time efficiency, the atom indexes are actu-
ally indexes into a coordinate array, so the actual atom index A is
calculated
from the coordinate array index N by A = N/3 + 1. (N is the value in the
topology file)
%FORMAT(10I8)
There are 3 × NBONH integers in this section.
BONDS WITHOUT HYDROGEN
This section contains a list of every bond in the system in which neither
atom
is Hydrogen. It has the same structure as BONDS INC HYDROGEN described
above.
%FORMAT(10I8)
There are 3 × NBONA integers in this section.
Following is the initial portion of my parm7 file (ambertools14):
FLAG
BONDS_WITHOUT_HYDROGEN
%FORMAT(10I8)
30 33 1 30 36 2 12 18
5 12
30 6 0 12 8 81 84 1
81 87
2 66 69 10 57 66 10 48
57 11
42 48 5 42 81 6 36 42
14 132
135 1 132 138 2 120 126 17
114 120
19 111 114 20 108 111 21 108
126 22
99 108 23 93 99 5 93 132
6 87
93 14 174 177 1 174 180 2
168 174
6 159 168 5 150 159 11 141
150 11
138 141 24 138 168 14 246 249
1 246
252 2 225 228 26 225 237 26
219 225
26 210 219 27 201 210 11 192
201 11
186 192 5 186 246 6 180 186
14 312
315 1 312 318 2 291 300 29
282 291
11 273 282 11 264 273 11 258
264 5
258 312 6 252 258 14 348 351
1 348
354 2 339 342 30 339 345 30
330 339
31 324 330 5 324 348 6 318
324 14
420 423 1 420 426 2 411 417
33 405
411 34 399 405 34 393 399 34
390 393
35 390 417 36 384 390 37 378
384 17
375 378 38 375 417 39 366 375
40 360
366 5 360 420 6 354 360 14
483 486
1 483 489 2 471 477 34 462
465 42
462 471 43 456 462 43 450 456
34 447
450 34 447 477 34 438 447 44
432 438
Could you please instruct me how to verify bonds in the above list for the
two initial residues in the corresponding PDB file?
ATOM 1 N ALA 1 39.886 -67.858 8.967 1.00 0.00
ATOM 2 H1 ALA 1 40.139 -66.882 8.910 1.00 0.00
ATOM 3 H2 ALA 1 39.435 -68.128 8.104 1.00 0.00
ATOM 4 H3 ALA 1 40.681 -68.381 9.306 1.00 0.00
ATOM 5 CA ALA 1 38.841 -68.004 10.020 1.00 0.00
ATOM 6 HA ALA 1 37.934 -68.417 9.578 1.00 0.00
ATOM 7 CB ALA 1 39.276 -69.022 11.092 1.00 0.00
ATOM 8 HB1 ALA 1 39.319 -68.531 12.064 1.00 0.00
ATOM 9 HB2 ALA 1 38.557 -69.840 11.130 1.00 0.00
ATOM 10 HB3 ALA 1 40.261 -69.416 10.841 1.00 0.00
ATOM 11 C ALA 1 38.486 -66.675 10.668 1.00 0.00
ATOM 12 O ALA 1 39.265 -65.721 10.620 1.00 0.00
ATOM 13 N MET 2 37.288 -66.634 11.251 1.00 0.00
ATOM 14 H MET 2 36.670 -67.430 11.184 1.00 0.00
ATOM 15 CA MET 2 36.788 -65.488 12.003 1.00 0.00
ATOM 16 HA MET 2 37.498 -64.664 11.926 1.00 0.00
ATOM 17 CB MET 2 35.425 -65.022 11.462 1.00 0.00
ATOM 18 HB2 MET 2 34.698 -65.828 11.565 1.00 0.00
ATOM 19 HB3 MET 2 35.087 -64.154 12.027 1.00 0.00
ATOM 20 CG MET 2 35.418 -64.613 9.987 1.00 0.00
ATOM 21 HG2 MET 2 35.721 -65.461 9.373 1.00 0.00
ATOM 22 HG3 MET 2 34.414 -64.298 9.701 1.00 0.00
ATOM 23 SD MET 2 36.551 -63.245 9.652 1.00 0.00
ATOM 24 CE MET 2 35.781 -61.890 10.516 1.00 0.00
ATOM 25 HE1 MET 2 36.464 -61.506 11.274 1.00 0.00
ATOM 26 HE2 MET 2 35.541 -61.096 9.808 1.00 0.00
ATOM 27 HE3 MET 2 34.866 -62.237 10.995 1.00 0.00
ATOM 28 C MET 2 36.619 -65.876 13.464 1.00 0.00
ATOM 29 O MET 2 36.237 -67.031 13.793 1.00 0.00
Embarrassed enough to pose such a naive question, however I am in trouble
in verifying the active center with transition metals (where not all bonds
indicated by both leap log and parmed.py are displayed on VMD; I know that
in such a case VMD only relies on bonds registered in the parm7 file,
abandoning any guess on interatomic distances)
Thanks a lot for your patience
francesco pietra
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Received on Thu Jan 15 2015 - 00:30:03 PST
