Hi Edo,
I don't know if this would be appropriate for your system, but at least it's
worth checking out.
Parameters for an anionic cysteine have already been determined according to
the descriptions of most force fields and are actually already built into
the residue libraries for most of the Amber force fields. The residue name
is CYM. If you simply change the names of the residues in your PDB file
from CYG to CYM, leap will read the built-in parameters and you don't even
need the CYG prep file.
Steve
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Ilyas Yildirim
Sent: Monday, September 24, 2007 5:54 PM
To: amber.scripps.edu
Subject: Re: AMBER: Help WARNING: The unperturbed charge of the unit
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 saccenti.cerm.unifi.it 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) =
= http://www.pas.rochester.edu/~yildirim/ =
---------------------------------------------------------------
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Received on Wed Sep 26 2007 - 06:07:16 PDT
