AMBER Archive (2007)

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

From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Thu Jan 04 2007 - 09:54:39 CST

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> 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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