AMBER Archive (2004)

Subject: AMBER: Amber7 tleap problem

From: Ed Pate (pate_at_math.wsu.edu)
Date: Sat Sep 04 2004 - 14:03:47 CDT

Hello:

I am trying to use Amber7 on the Xeon cluster at NCSA to do a molecular
dynamics simulation on a protein. Amber7 was installed by NCSA personnel.
My command script (interactive mode) to generate the .top and .crd files
from the .pdb file is

tleap
source leaprc.ff94
xxx = loadpdb abc.pdb
saveamberparm xxx abc.top abc.crd
quit

No error messages are flagged to the terminal. However, the leap.log file
contains the following warning messages. The .pdb file is large and there
are actually >100 of the warnings. The list is a representative stretch.

** 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

Can anyone help me to understand what is going on?

Thanks,

Ed Pate

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