From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Fri Mar 08 2019 - 10:51:43 CST
Hi Shreyas,
I think NAMD may be expecting atoms in QM-MM bonds to appear sequentially
in the PDB file (which is clearly a bad assumption given your example). If
this is really the case, there is no immediate workaround that I can think
of.
I'll need to check some more, but I'll get back to the list next week.
Best,
Marcelo
--- Marcelo Cardoso dos Reis Melo, PhD Postdoctoral Research Associate Luthey-Schulten Group University of Illinois at Urbana-Champaign crdsdsr2_at_illinois.edu +1 (217) 244-5983 On Mon, 4 Mar 2019 at 05:56, shreyas supekar <shreyas.supekar_at_gmail.com> wrote: > 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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