AMBER Archive (2006)

Subject: Fwd: Fwd: AMBER: LEaP error : unbalanced charge

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Fri Jun 16 2006 - 12:28:08 CDT

Dear Thomas

I am not sure that I had done right for deprotonate tyrosine. But I can only
give you some details that I try to check this charge. I see the partial
charge from WeblabViewer and it has decrease comparing with regular
tyrosine. For the prepin file, I see this charges do not have the same
charge. I think this charge from prepin file should be ok. Besides, I had
already edited atom C and O (C=O)that link the peptide bond with N-H to link
the peptide bond. I mean I found the peptide bond breaking down when I do
LEaP without C-O modified. So I decide to change C2-O5 to C-O to every
parameter files generated by antechamber. This can link this peptide bond.
Hopefully all of these details maybe give you an idea that why I do wrong
with this charges. Maybe, this is not the way to do RESP charge. Therefore,
please tell me the the right one.

Thanks

Jitrayut

---------- Forwarded message ----------
From: Thomas Steinbrecher <steinbrt_at_scripps.edu>
Date: 16 ÁÔ.Â. 2006, 23:45 ¹.
Subject: Re: Fwd: AMBER: LEaP error : unbalanced charge
To: jitrayut jitonnom <jitrayut.018_at_gmail.com>

Hi,

you should have created a .lib or .prep file for your new residue. Load
this into leap and edit it. You can set leap to display the charges for
you.

Regards,

Thomas
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