When running tleap to process a protein, I get the following results at the end of the run:
> saveamberparm ewsfli1 ewsfli1_noNaCl.prmtop ewsfli1_noNaCl.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 243 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
CGLU 1
NPRO 1
WAT 29492
)
(no restraints)
> quit
Quit
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
I do not know what to do about the:
CGLU 1
NPRO 1
Information. What does this mean and how do I deal with it?
The Building Protein Systems in Explicit Solvent tutorial indicates that, after running H++, the AMBER compatible PDB (PQR) structure in predicted protonation state should be examined and GLU should be replaced with GLH. Is that what needs to be done about the CGLU output?
What about the NPRO output?
All suggestions appreciated. If additional information is required, I'd be happy to provide it.
Happy New Year!
Jim Kress
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Received on Sat Dec 30 2023 - 22:30:03 PST
