On Thu, Feb 26, 2009, Sampath Koppole wrote:
>
> Everything seems normal on the screen-log (pasted below !!) but in the leap.log file that was created,
> I have a few errors like the following when I save the prmtop and the initial coordinates:
> -----------------------------------------------------------------------------------------------------------
> > saveamberparm bvc bvc/bvc.prmtop bvc/bvc.inpcrd
> Checking Unit.
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> ** 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 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 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
> total 488 improper torsions applied
> Building H-Bond parameters.
> Not Marking per-residue atom chain types.
> Marking per-residue atom chain types.
> (Residues lacking connect0/connect1 -
> these don't have chain types marked:
>
> res total affected
>
> WAT 6791
> )
> (no restraints)
These are not errors, just informational messages. You should be able
to proceed.
...dac
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Received on Fri Feb 27 2009 - 01:16:28 PST
