AMBER Archive (2009)

Subject: Re: [AMBER] Leap warning

• Previous message: case: "Re: [AMBER] parameterization of protein-ligand complex"
• Maybe in reply to: manoj singh: "[AMBER] Leap warning"
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> ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
> atoms are: CG CE2 CD2 CE3

This is a planar conformation with no improper torsion to
stiffen the planarity. It has nothing to do with the quality
of your pdb file. If there is a custom residue involved, you
may want to look at dynamics to see if these atoms are too
floppy, to decide whether adding an improper torsion term is
advisable (also you could consider how confident you are in
assigning atom types). I don't have a sense for how often this
is the case. Ideally we would have a list of 0-energy impropers
to block this message from appearing in cases where it is
irrelevant.

Bill

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• Previous message: case: "Re: [AMBER] parameterization of protein-ligand complex"
• Maybe in reply to: manoj singh: "[AMBER] Leap warning"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]