Dear All,
We are preparing a ligand for Thermodynamic integration, but getting the
following error.
The tutorial for TI run successfully but was unable to run for the ligands
(the only change in structure is the R group with piperidine and morpholine
ring). Instead of carbon in piperidine ring is replaced by oxygen. Giving
error: *Atom coordinate disagreement*
Can you please suggest what might be the source of this error?
Looking forward to valuable suggestions from the list.
Thank you and best regards.
Softcore Mask :1.O2; matches 1 atoms
this run corresponds to V1, its softcore atoms interact fully for
lambda=1
this process: 3991 atoms, partner process: 3993 atoms
Checking for mismatched coordinates.
WARNING: Local coordinate 1 differs from partner coordinate 1 !
Deviation is small, using partner coordinate.
WARNING: Local coordinate 2 differs from partner coordinate 2 !
Deviation is small, using partner coordinate.
WARNING: Local coordinate 3 differs from partner coordinate 3 !
Deviation is small, using partner coordinate.
WARNING: Local coordinate 4 differs from partner coordinate 4 !
Deviation is small, using partner coordinate.
WARNING: Local coordinate 5 differs from partner coordinate 5 !
Deviation is small, using partner coordinate.
WARNING: Local coordinate 6 differs from partner coordinate 6 !
Deviation is small, using partner coordinate.
WARNING: Local coordinate 7 differs from partner coordinate 7 !
Deviation is small, using partner coordinate.
WARNING: Local coordinate 8 differs from partner coordinate 8 !
Deviation is small, using partner coordinate.
WARNING: Local coordinate 9 differs from partner coordinate 9 !
Deviation is small, using partner coordinate.
... making more adjustments ...
WARNING: Local coordinate 58 differs from partner coordinate 58 !
SANDER BOMB in subroutine sc_check_and_adjust
Atom coordinate disagreement
Check input files.
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Received on Thu Mar 24 2022 - 23:00:03 PDT
