As long as you load an old prep file, you will be informed about
the hard-coded improper torsions in it.
If you save your template to mol2 format, and load that version
in future, you won't get the messages, which are for debugging
improper torsion assignments.
Note that the prep impropers are not used except in this context.
Bill
Andrew Voronkov <drugdesign.yandex.ru> wrote:
> Dear Amber users,
> I was using prep file in prepin format for the small molecule ligand in complex with protein.
> Parameter and residue files were saved ok, but a notice about the old prep form was shown.
> What is the reason for it? (part of the small molecule is shown below) How to avoid such
> messages?
>
> Sincerely yours,
> Andrey
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> old PREP-specified impropers:
> " <HE1 133>: O CA N H
> <HE1 133>: CE1 CD2 NE2 HE2
> <HE1 133>: CG NE2 CD2 HD2
> <HE1 133>: ND1 NE2 CE1 HE1
> <RES 212>: C13 C3 C1 H1
> <RES 212>: C1 C15 C3 H3"
> .....
>
> .....
>
> "<RES 212>: C7 C8 C17 O2
> <RES 212>: C17 C6 C8 H8
> <RES 212>: C16 C8 C6 H6"
> total 746 improper torsions applied
> 26 improper torsions in old prep form
> 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
>
> CGLU 1
> NGLY 1
> WAT 5879
> )
> (no restraints)
>
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Jan 10 2012 - 12:30:03 PST
