AMBER Archive (2003)

Subject: Re: AMBER pdb help - lost atoms

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Tue Apr 01 2003 - 16:21:46 CST

Hi,

The e-mail below just reminded me that I have got the following warnings
when I save a structure in Leap (with saveAmberParm):

 ** Warning: No sp2 improper torsion term for H-H-N3-H
        atoms are: H1 H2 N H3
 ** Warning: No sp2 improper torsion term for H-H-N3-CT
        atoms are: H1 H2 N CA
 ** Warning: No sp2 improper torsion term for H-H-N3-CT
        atoms are: H1 H3 N CA
 ** Warning: No sp2 improper torsion term for H-H-N3-CT
        atoms are: H2 H3 N CA
 ** Warning: No sp2 improper torsion term for CT-H-N3-H
        atoms are: CE HZ1 NZ HZ2
 ** Warning: No sp2 improper torsion term for CT-H-N3-H
        atoms are: CE HZ1 NZ HZ3
 ** Warning: No sp2 improper torsion term for CT-H-N3-H
        atoms are: CE HZ2 NZ HZ3
 ** Warning: No sp2 improper torsion term for H-H-N3-H
        atoms are: HZ1 HZ2 NZ HZ3

What do these warning mean exactly and how important are they? (I am using
the parm94 force field for this structure). One common thing is that all
of the improper torsions contain hydrogen atoms so if I use Shake in my
simulations these warnings are really unimportant?

Thank you,
Ioana

On Tue, 1 Apr 2003, David A. Case wrote:

> The general "do" for leap is this: keep editing your input pdb file until
> LEaP no longer complains. Pay careful attention to any messages you get
> when invoking the loadPdb command. Use the xleap viusalizer to see if the
> unit you have loaded in looks correct (use the bondbydistance command if you
> don't have standard residues).
>
> ..good luck...dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> 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 | http://www.scripps.edu/case
> ==================================================================
>
>