[gmx-users] define a new residue

Shima Arasteh shima_arasteh2001 at yahoo.com
Mon Jul 9 13:37:25 CEST 2012

Hi :)
I got the parameters of the first 3 residues of the peptide and when I got 0.008e for total charge of the first 2 residues ( formyl and valine). It is expected to be zero. 

Is the 0.008e acceptable? Or I look for an other way to get the correct parameters and charges?

Thaankkkkkkkkkkkkkks! :)


From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Monday, July 9, 2012 12:35 AM
Subject: Re: [gmx-users] define a new residue

On 7/8/12 12:43 PM, Shima Arasteh wrote:
> OK.
> What about generating an output file through CGenFF by the first 3 residues of the protein, rather thn the first 2 (formyl+valine)?

Maybe.  Try it and see, rather than waiting a few hours for someone to get around to replying :)


-- ========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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