[AMBER] Atom coordinate disagreement error in running the TI calculation

From: Bhakti Hirlekar <mc2020-1001phd.niperguwahati.in>
Date: Fri, 25 Mar 2022 11:03:59 +0530

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
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