Re: AMBER: Help WARNING: The unperturbed charge of the unit

From: Ilyas Yildirim <>
Date: Mon, 24 Sep 2007 17:53:40 -0400 (EDT)

Dear Edo,

You have created a new CYG residue and new charge parameter for CU atom.
The new CYG residue has a total charge of -0.698, and CU is 0.396. In
your inpdb file, you have 3 CYG, and 1 CU, and when you add them up, the
total charge of the system is -1.698000.

Where did you get these parameters? Also, do you know what the total
charge of your structure is? The new CYG residue - I guess - should
have a -1 charge (The title of the CYG_prep is 'CYSTEINE with negative
charge'). You might want to follow the resp procol to calculate the
resp charges for your new CYG residue.

I cant say too much about your system, or what to do with the 3 CYG - Cu
region, but the reason why you see noninteger number is due to the charges
defined for CYG and CU.

Good luck,

On Mon, 24 Sep 2007 wrote:

> Dear All,
> I'm getting the following
> Checking Unit.
> WARNING: There is a bond of 3.363639 angstroms between:
> ------- .R<CYG 87>.A<SG 8> and .R<CU 148>.A<CU 1>
> ERROR: The unperturbed charge of the unit: -1.698000 is not integral.
> WARNING: The unperturbed charge of the unit: -1.698000 is not zero.
> -- ignoring the error and warnings.
> I'm aware that the total charge must be equal to zero
> and also think that this must depend or on CGY or Cu or on both.
> I browsed the amber archive and tried several suggestion, but I'm still
> getting that error
> Does somebody as some idea on how to fix this bug?
> I attach the files I'm using
> Many thanks
> edo

  Ilyas Yildirim
  = Department of Chemistry      -                              =
  = University of Rochester      -                              =
  = Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) =
  =                     =
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Received on Wed Sep 26 2007 - 06:07:07 PDT
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