AMBER Archive (2004)

Subject: Re: AMBER: warning about improper dihedral in leap!!

From: David A. Case (
Date: Thu Apr 08 2004 - 10:09:11 CDT

On Thu, Apr 08, 2004, Pradipta Bandyopadhyay wrote:

> My pdb file has a protein and a ligand (no
> bond between these).
> I made a prepi file for the ligand using antechamber.
> When I try to save the .top and .crd file in Leap
> ( I am using parm99.dat)
> using saveAmberParm I am getting the following warnings.
> --------------------------------------------------------
> ** Warning: No sp2 improper torsion term for H-H-N3-CT
> atoms are: H2 H3 N CD

Does this behavior depend on having a ligand? Would you get similar warnings
if you just constructed a pure protein (with no ligand)? I ask this because
the atom types listed above look like protein atoms(?). Ligand atom types
created by antechamber would ordinarily have lower case names.

What version of Amber do you have, and which input files are you using? You
can check your "leap.log" file to look for any evidence that N3 is being
assigned as an sp2 atom.

Generally, such warnings can be ignored, but one problem (the wrong
hybridization for N3) might be suggestive that other problems exist, and so
it might be good to track this down.



================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to