Re: FATAL ERROR: Error in QM-MM bond assignment; bonded QM atoms with occupancy=1

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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