Hello,
I tried building the structure from scratch in tleap using the following command
AbSOD-15aa-modified = sequence { ACE TRP GLU HID ALA TYR TYR ILE ASP PHE ARG ASN LEU ARG PRO LYS NHE}
and the output structure is correct when I viewed it in chimera.
But when I tried to save the parm7 and rst7 files after solvating the peptide, I got these messages.
saveamberparm AbSOD-15aa-modified parm7 rst7
Checking Unit.
Warning: The unperturbed charge of the unit (1.000000) is not zero.
Note: Ignoring the warnings from Unit Checking.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 73 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
ACE 1
NHE 1
)
(no restraints)
Should I fix the charge of the system so it is 0 before doing anything else? Like try adding Cl- ion to neutralize it?
I also don't know if the ACE 1 and NHE1 not being recognized is going to cause a big problem in the simulation.
Thank you.
Yen Nguyen
Graduate Research Assistant
George Mason University
Department of Chemistry and Biochemistry
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Received on Mon Dec 13 2021 - 14:30:02 PST
