From: shreyas supekar (shreyas.supekar_at_gmail.com)
Date: Mon Mar 04 2019 - 05:53:17 CST
Hello all,
I am having trouble setting up QM/MM boundary. The system in question has
two bonded atoms (CA and CB; beta=1, occupancy=1) in QM region, and the
sidechain of the residue (beta=0;occupancy=1) and the backbone in MM region
(beta=0;occupancy=1). This causes an error in the QM/MM setup as NAMD tries
to assign CA and CB to MM region. Is there a way to prevent CA-CB bond
assignment? Can I alternatively supply bondlist pairs (as in psf files)
rather than using the occupancy column?
Please find an explanation of the problem and associated error below.
Thanks,
Shreyas
---------------------
QM/MM topology:
### rest of QM
|
### -(0=C)--|--CA-CB--|--sc ###
### ^ ^ ^ ^
### MM | QM QM | MM ###
PDB with assigned beta and occupancy columns
ATOM 510 N TYR P 36 5.856 30.161 22.979 0.00 1.00 P0
N
ATOM 511 HN TYR P 36 6.235 30.419 22.093 0.00 1.00 P0
H
ATOM 512 CA TYR P 36 4.593 30.567 23.249 *1.00 1.00*
P0 C
ATOM 513 HA TYR P 36 4.186 29.925 23.995 0.00 1.00 P0
H
ATOM 514 CB TYR P 36 4.432 32.053 23.655 *1.00 1.00*
P0 C
ATOM 515 HB1 TYR P 36 4.995 32.205 24.537 0.00 1.00 P0
H
ATOM 516 HB2 TYR P 36 4.811 32.706 22.806 0.00 1.00 P0
H
ATOM 517 CG TYR P 36 3.052 32.542 24.069 *1.00 0.00*
P0 C
ATOM 518 CD1 TYR P 36 2.341 31.925 25.056 0.00 0.00 P0
C
ATOM 519 HD1 TYR P 36 2.575 30.967 25.428 0.00 0.00 P0
H
ATOM 529 C TYR P 36 3.691 30.306 21.997 *1.00 0.00*
P0 C
ATOM 530 O TYR P 36 3.910 30.779 20.906 0.00 0.00 P0
O
Error:
>ERROR: Atoms 513 and 511 are assigned as QM atoms.
>FATAL ERROR: Error in QM-MM bond assignment.
ᐧ
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