AMBER Archive (2008)

Subject: Re: AMBER: Charge neutralization, GlcNac & GalNac improper torsional angles from old PREP

From: Bill Ross (
Date: Fri Jul 25 2008 - 15:40:27 CDT

> Hi AMBER users,
> I am using AMBER_9 ( Glycam04) and i got a warning about the *improper
> torsional angles *from *xleap *while using GlcNac & GalNac sugar units. The
> xleap output is as follows :
> *> saveamberparm ec e2is_g.crd
> Checking Unit.
> **ERROR: The unperturbed charge of the unit: -12.710158 is not integral.
> WARNING: The unperturbed charge of the unit: -12.710158 is not zero.**
> -- ignoring the error and warning.
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.*
> *
> **old PREP-specified impropers:
> **<WYB 242>: C2 C2N N2 H2N
> <WYB 242>: CME N2 C2N O2N
> <4YB 244>: C2 C2N N2 H2N
> <4YB 244>: CME N2 C2N O2N
> <1VA 249>: C2 C2N N2 H2N
> <1VA 249>: CME N2 C2N O2N**

Prep-specified impropers are kept for reference when loading a residue
in format. They are printed on the assumption that the
has defined the correct impropers in its IMPROPER section. When all
residues have been loaded this way it gives a cross-check on leap's
'place impropers wherever the topology matches parameters in the force
field' policy.

> total 1524 improper torsions applied
> 6 improper torsions in old prep form

In this case, it appears that only 3 residue templates were loaded from files, so the cross check is irrelevant.

So there is nothing to worry about.


> 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 2
> NVAL 2
> )
> (no restraints)
> >*
> What does the message "*old PREP-specified impropers*" mean?
> Are there possible corrections that can be made in this regard?
> What might be the implications of this (if this is a problem) in the MD
> simulations (if performed without any changes)? *
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