AMBER Archive (2007)

Subject: Re: AMBER: The unperturbed charge of the unit: -20.999999 is not zero.

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Thu Jan 04 2007 - 13:31:29 CST

I think it's better to say that you MIGHT want to add counterions.
You do not have to do this, but you should be aware that the system
is not neutral and make the appropriate decision about whether or not
to add counterions.

Nitin Bhardwaj wrote:

> Your system is not neutral. You have to add positive counterions. You
> can add Na+ ions by using "addions" command. Just type addions to see
> how it is used. You have to add 21 Na+.
>
> On 04/01/07, *saurabh agrawal* <imsam100_at_yahoo.co.in
> <mailto:imsam100_at_yahoo.co.in>> wrote:
>
> Dear Friends,
> After running the following command, I got the
> following WARNING.
>
> saveamberparm s s.top s.crd
> Checking Unit.
> WARNING: The unperturbed charge of the unit:
> -20.999999 is not zero.
>
> -- ignoring the warning.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> old PREP-specified impropers:
> <MOL 23>: C38 C30 C31 O32
> <MOL 23>: C41 N29 C28 O32
> <MOL 23>: C31 C33 C30 N29
> <MOL 23>: C30 N34 C33 O37
> <MOL 23>: C39 C35 C36 O37
> <MOL 23>: C36 C5 C35 N34
> <MOL 23>: C35 N1 C5 O4
> <MOL 23>: C2 H3 C3 O4
> <MOL 23>: C26 C3 C2 N1
> <MOL 23>: C2 N27 C26 O25
> <MOL 23>: C23 H24 C24 O25
> <MOL 23>: C24 C10 C23 N27
> <MOL 23>: C23 N6 C10 O9
> <MOL 23>: C7 H8 C8 O9
> <MOL 23>: C12 C8 C7 N6
> <MOL 23>: C7 N13 C12 O11
> <MOL 23>: C14 H15 C15 O11
> <MOL 23>: C15 C16 C14 N13
> <MOL 23>: C14 N17 C16 O20
> <MOL 23>: C18 H19 C19 O20
> <MOL 23>: C19 C21 C18 N17
> <MOL 23>: C18 N42 C21 S22
> total 128 improper torsions applied
> 22 improper torsions in old prep form
> Building H-Bond parameters.
> Not Marking per-residue atom chain types.
> Marking per-residue atom chain types.
> (no restraints)
>
>
> If some could tell me the way to get out of this
> WARNING, I shall be highly thankful to him/ her.
> Can i ignore this warning?
>
>
> saurabh
>
>
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>
>
> --
> $B&-(BI+I$B'*(B

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