AMBER Archive (2008)

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

From: Bill Ross (ross_at_cgl.ucsf.edu)
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.top 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 prep.in format. They are printed on the assumption that the prep.in
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
prep.in files, so the cross check is irrelevant.

So there is nothing to worry about.

Bill

> 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)? *
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu