AMBER Archive (2004)

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

From: Pradipta Bandyopadhyay (pradipta_b_at_mail.jnu.ac.in)
Date: Thu Apr 08 2004 - 06:50:18 CDT

Hi,

  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
 ** Warning: No sp2 improper torsion term for H-H-N3-CT
        atoms are: H2 H3 N CA
 ** Warning: No sp2 improper torsion term for H-CT-N3-CT
        atoms are: H2 CD N CA
 ** Warning: No sp2 improper torsion term for H-CT-N3-CT
        atoms are: H3 CD N CA
 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
        atoms are: CG CE2 CD2 CE3
 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
        atoms are: NE1 CZ2 CE2 CD2
 ** 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
 ** 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
 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
        atoms are: CG CE2 CD2 CE3
 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
        atoms are: NE1 CZ2 CE2 CD2
 ** 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

and Finally it says
old PREP-specified impropers:
 <199>: C6 C1 C7 C8
 <199>: C3 C7 C1 O2
 <199>: C4 C1 C3 H80
 <199>: C3 C5 C4 H81
 <199>: C4 C6 C5 H82
 <199>: C9 C5 C6 C7
 <199>: C6 N11 C9 O10
 <199>: C15 C19 C14 C13
 <199>: C14 C16 C15 H89
 <199>: C15 C17 C16 H90
 <199>: C16 C18 C17 H91
 <199>: C17 C19 C18 H92
 <199>: C14 C18 C19 H93
 <199>: C20 N24 C22 O23
 <199>: C30 N33 C31 O32
 <199>: C36 C40 C35 C34
 <199>: C35 C37 C36 C41
 <199>: C36 C38 C37 H107
 <199>: C37 C39 C38 H108
 <199>: C38 C40 C39 H109
 <199>: C35 C39 C40 H110
 total 575 improper torsions applied
 21 improper torsions in old prep form

------------------------------------------------
It does save the .top and .crd files.

What are those warnings? Is anything wrong?

no SP2 improper for H-H-N3-CT is not clear to me since
both N3 and CT are SP3.

           Pradipta

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