From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Dec 12 2015 - 09:09:55 CST
Hello:
As far as I can remember, NAMD does not read the element column in the pdb
file prepared with psfgen.
Even if true, why VMD (1.9.2 Linux in text mode) does not fully build the
element column of CYS CYSD patched
ATOM 7589 C HSD A 502 -9.956 31.185 -18.889 1.00 0.00
PRA C
ATOM 7590 O HSD A 502 -10.454 31.249 -20.013 1.00 0.00
PRA O
ATOM 7591 N CYS A 503 -8.702 30.797 -18.663 1.00 0.00
PRA N
ATOM 7592 HN CYS A 503 -8.361 30.759 -17.713 1.00 0.00
PRA H
ATOM 7593 CA CYS A 503 -7.905 30.157 -19.699 1.00 0.00
PRA C
ATOM 7594 HA CYS A 503 -7.913 30.790 -20.584 1.00 0.00
PRA H
ATOM 7595 CB CYS A 503 -6.462 29.977 -19.236 1.00 0.00
PRA
ATOM 7596 HB1 CYS A 503 -6.017 30.961 -19.091 1.00 0.00
PRA
ATOM 7597 HB2 CYS A 503 -6.440 29.431 -18.291 1.00 0.00
PRA
ATOM 7598 SG CYS A 503 -5.529 29.081 -20.452 1.00 0.00
PRA
ATOM 7599 C CYS A 503 -8.506 28.785 -19.988 1.00 0.00
PRA C
ATOM 7600 O CYS A 503 -8.925 28.083 -19.061 1.00 0.00
PRA O
and CYM
ATOM 46 N CYM A 4 -36.415 29.381 -46.642 1.00 0.00
PRA N
ATOM 47 HN CYM A 4 -35.975 29.520 -45.744 1.00 0.00
PRA H
ATOM 48 CA CYM A 4 -35.816 29.990 -47.828 1.00 0.00
PRA C
ATOM 49 HA CYM A 4 -36.195 29.506 -48.728 1.00 0.00
PRA H
ATOM 50 CB CYM A 4 -36.182 31.474 -47.915 1.00 0.00
PRA
ATOM 51 HB1 CYM A 4 -35.625 31.955 -48.719 1.00 0.00
PRA H
ATOM 52 HB2 CYM A 4 -37.242 31.549 -48.160 1.00 0.00
PRA H
ATOM 53 SG CYM A 4 -35.921 32.354 -46.370 1.00 0.00
PRA
ATOM 54 C CYM A 4 -34.294 29.804 -47.881 1.00 0.00
PRA C
ATOM 55 O CYM A 4 -33.602 30.512 -48.604 1.00 0.00
PRA O
(which are graphically perfectly built)?
francesco pietra
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