On Fri, Nov 23, 2007, sanket deshmukh wrote:
> I have modified the structure and used only one molecule (26 atom the
> way you suggested to me). It is relaxed now but still I am facing the
> same problem regarding the connectivity.
[The "same problem" is that antechamber can't assign atom and bond types.]
I'll admit this is wierd. I'm cc-ing to Junmei to see if he can spot the
problem. Here is the input pdb file that antechamber can't handle:
ATOM 1 C 1 7.397 10.474 12.292
ATOM 2 H11 2 7.849 10.392 13.319
ATOM 3 H12 3 7.130 9.435 11.964
ATOM 4 C1 4 8.397 11.095 11.349
ATOM 5 H1 5 8.716 12.098 11.723
ATOM 6 H2 6 9.298 10.440 11.274
ATOM 7 H3 7 7.964 11.224 10.325
ATOM 8 C2 8 6.159 11.307 12.420
ATOM 9 O1 9 5.923 12.116 13.318
ATOM 10 O2 10 5.093 11.213 11.552
ATOM 11 C3 11 5.191 10.460 10.350
ATOM 12 H4 12 4.319 9.752 10.378
ATOM 13 H5 13 6.151 9.892 10.260
ATOM 14 C4 14 5.030 11.417 9.168
ATOM 15 H6 15 4.468 10.917 8.337
ATOM 16 H7 16 4.500 12.351 9.491
ATOM 17 O3 17 6.353 11.728 8.728
ATOM 18 C5 18 6.495 12.614 7.683
ATOM 19 O4 19 7.680 12.833 7.431
ATOM 20 C6 20 5.289 13.166 6.994
ATOM 21 H14 21 4.726 12.309 6.535
ATOM 22 H15 22 4.620 13.647 7.757
ATOM 23 C7 23 5.662 14.168 5.931
ATOM 24 H8 24 6.395 13.724 5.215
ATOM 25 H9 25 4.750 14.484 5.371
ATOM 26 H10 26 6.134 15.069 6.393
CONECT 1 4 3 8 2
CONECT 2 1
CONECT 3 1
CONECT 4 7 5 1 6
CONECT 5 4
CONECT 6 4
CONECT 7 4
CONECT 8 10 1 9
CONECT 9 8
CONECT 10 11 8
CONECT 11 13 12 10 14
CONECT 12 11
CONECT 13 11
CONECT 14 16 17 15 11
CONECT 15 14
CONECT 16 14
CONECT 17 18 14
CONECT 18 20 19 17
CONECT 19 18
CONECT 20 23 21 22 18
CONECT 21 20
CONECT 22 20
CONECT 23 24 25 20 26
CONECT 24 23
CONECT 25 23
CONECT 26 23
END
....dac
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Received on Sun Nov 25 2007 - 06:07:46 PST
