Hello,
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.
I checked, all the atoms and residues are contiguous.
The atoms that make the dihedral mentioned in the message belong to different molecules:
ATOM 12082 O33 H6P 760 -11.874 11.205 -21.029 1.00 0.00
ATOM 12083 H01 H6P 760 -10.539 7.276 -23.570 1.00 0.00
ATOM 12084 H02 H6P 760 -11.474 7.950 -24.997 1.00 0.00
ATOM 12085 H04 H6P 760 -11.670 9.946 -24.096 1.00 0.00
ATOM 12086 H05 H6P 760 -10.735 8.696 -20.085 1.00 0.00
ATOM 12087 H06 H6P 760 -10.740 7.450 -21.211 1.00 0.00
ATOM 12088 H07 H6P 760 -9.350 8.629 -20.950 1.00 0.00
ATOM 12089 H08 H6P 760 -10.718 11.682 -22.491 1.00 0.00
ATOM 12090 H09 H6P 760 -9.885 11.173 -21.002 1.00 0.00
ATOM 12091 H10 H6P 760 -12.482 10.448 -21.094 1.00 0.00
TER
ATOM 12092 N ARG 761 0.584 -2.696 8.874 1.00 0.00
ATOM 12093 H1 ARG 761 0.918 -3.215 9.673 1.00 0.00
I wanted to add that when I reverse the order of the molecules, i.e., I construct a mutation from Thr to Ala everything works OK.
However, the atom numbers in the scmask1 and scmask2 are incorrect. This can be fixed easily, but this also needs attention.
Hope this helps. If you need the files where this occurs, I’ll gladly send or upload them.
Thanks,
Roman Osman
Professor
Department of Pharmacological Sciences
Icahn School of Medicine at Mount Sinai
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Received on Thu Sep 05 2024 - 07:30:01 PDT
