Hello,
I sent the message below about a week ago, and did not receive a response.
Can someone take a look at it.
Thanks
Roman Osman
I suspect there is an error in tiMerge.
I wanted to construct a mutation of a protein and a complex in which an Ala is mutated to Thr.
I created the protein_ala.pdb, protein_thr.pdb and the ligand (h6p).
I created with tleap the protein.parm7 and protein.rst7 that contain the protein_ala.pdb followed by protein_thr.pdb with ions and solvated in a box.
Similarly, I created the complex.
Then I ran the tiMerge in ParmEd:
I get this error message:
ParmEd: a Parameter file Editor
Loaded Amber topology file protein.parm7
Reading input from STDIN...
> Loading restart file protein.rst7
> Files are overwritable
> Merging molecules [:1-760] [:761-1520] with sc mask [:690] [:1450]
AmberWarning: Molecule atoms are not contiguous! Attempting to reorder to fix.
Action tiMerge failed
TiMergeError: Cannot have dihedral cross through softcore region. (DIHED : 12091 12092 12093 12082). 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.
Roman Osman
Professor
Department of Pharmacological Sciences
Icahn School of Medicine at Mount Sinai
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Received on Fri Sep 20 2024 - 10:00:07 PDT
