AMBER Archive (2008)

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

From: Sandeep Kaushik (
Date: Fri Jul 25 2008 - 05:04:11 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**

total 1524 improper torsions applied
6 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

(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)? *
Kindly direct me to the possible solutions.


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