AMBER Archive (2007)

Subject: RE: AMBER: Help WARNING: The unperturbed charge of the unit

From: saccenti_at_cerm.unifi.it
Date: Tue Sep 25 2007 - 07:23:25 CDT

Hi Steve,

I indeed found out this solution: in CYM the net charge is -1
I can prepare a CU(I) prep file with charge +1 so that the total charge
is -1x3 + 1 = -2.

I'm pretty new to this, but I have been warned that charges must be
distribuited over all the atoms of the complex:

                           (-1)CYG CYG(-1)
                                  \Cu(+1)/
                                    |
                                   CYC(-1)

I do not know if this is correct

The parameters I was using comes from CYG-Cu-CYG and in that case the sum
over the Cu and CYG charges is indeed -1

For the moment I'm using the same approach you kindly suggested but I'm
also looking for some reliable information about charge redistribution in
a such system with 3 cysteines and a copper(I)

Any more details or suggestion is more than welcome

Greets
Edo

> 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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of
> Ilyas Yildirim
> Sent: Monday, September 24, 2007 5:54 PM
> To: amber_at_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_at_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/ =
> ---------------------------------------------------------------
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> 

-- 
Dr Edoardo Saccenti
CERM Magnetic Resonance Center
University of Florence
Fiorgen Foundation
Via Luigi Sacconi n° 6
50019 Sesto Fiorentino
(FI) Italy
Tel: +39 055 4574281

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu