Dear Amber Community,
TiMerge in ParmEd is throwing an error whenever my system has periodic boundaries defined.
My TiMerge command is:
tiMerge :1-616 :617-1232 .3637-3639|.8026-8035 @12415-12424|.16811-16813 tol 0.1
If I use a parm7 with (1) no box and no solvent or (2) with solvent molecules but no box, I get:
timask1='.3637,3638,3639,8026,8027,8028,8029,8030,8031,8032,8033,8034,8035',
timask2='.8779,8780,8781,8782,8783,8784,8785,8786,8787,8788,8789,8790,8791',
scmask1='.3637,3638,3639,8026,8027,8028,8029,8030,8031,8032,8033,8034,8035',
scmask2='.8779,8780,8781,8782,8783,8784,8785,8786,8787,8788,8789,8790,8791’,
But If I use a parm7 that has (3) the box defined but no solvent, or (4) the box and solvent defined, I get
AmberWarning: Molecule atoms are not contiguous! I am attempting to reorder the atoms to fix this.
Action tiMerge failed
TiMergeError: Cannot have dihedral cross through softcore region. (DIHED : 8024 8026 8034 8046). Usually this means you have defined the softcore region in a way that breaks a ring. Try redefining your softcore region to include the ring or at least three consecutive atoms.
Why does the error message only appear when I have a periodic box defined? This issue makes completely no sense to me.
Can anyone please, please help?
Best,
Matthew
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Received on Sun Aug 21 2022 - 22:00:04 PDT
