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 - 03:43:03 CDT

I got this parameters files form a colleague.
First I tought that some H was missing but last night I realized
that the bug could be in the CYC and Cu prep files.

I'm now trying to get correct prep file for this two types

Many Thanks
Edo

> 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/ =
> ---------------------------------------------------------------
>
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-- 
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

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