From owner-chemistry@ccl.net Thu Dec 13 10:54:01 2007
From: "Saif Ullah sullah-#-ruc.dk" <owner-chemistry###server.ccl.net>
To: CCL
Subject: CCL: Convergence failure -- run terminated
Message-Id: <-35840-071213095416-16620-+D1IAzVPPgWw3z0cvnJZMg###server.ccl.net>
X-Original-From: Saif Ullah <sullah_+_ruc.dk>
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Date: Thu, 13 Dec 2007 15:01:48 +0100
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Sent to CCL by: Saif Ullah [sullah||ruc.dk]
Hi Kerwin,
          Thanks for useful suggestions.Yes, I am interested to optimize proton
between formamide and amino residue. The system with charge neutral by removing
one hydrogen from the Lysine sidechain, does work but I am also interested to
optimize the geometry with charge on side chain amine of Lysine. I have set the
charge to "1" and also multiplicity to "1", this input job is running at the
moment.


Saif

Quoting Kerwin D Dobbs <Kerwin.D.Dobbs%x%usa.dupont.com>:

> Sullah,
>
> I'm not a bio person, but it seems that you are looking at
> the H-bond between formamide and a much larger molecule.
> My guess is that this system should be charge neutral, and
> all the electrons should be paired (closed-shell computation
> rather than open-shell). Yet you have set the multiplicity
> of the system to be a doublet:
>
>  Symbolic Z-matrix:
>  Charge =  0 Multiplicity = 2
>                            ^^^
> If you want to see this calculation to completion, you need
> to do 2 things. First, set the multiplicity to "1". Next, you
> need to alter the structure of your "larger molecule" by
> removing a hydrogen from the terminal amino group, i.e.:
>
> R-CH2-CH2-NH3  change to  R-CH2-CH2-NH2
>
> Now, if you truly mean for this amino group to have the extra
> hydrogen, then the entire system must have a positive charge,
> i.e.,
>
>  Symbolic Z-matrix:
>  Charge =  1 Multiplicity = 1
>
> From my point-of-view, since you are doing a gas-phase
> computation, then you should remove the extra hydrogen and
> make the system neutral (Charge = 0).
>
> Kerwin
> ========================================
>  Kerwin Dobbs, Computational Chemist
>  DuPont CR&D
>  Information & Computing Technologies
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>  Kerwin.D.Dobbs%x%usa.dupont.com
>  http://www.linkedin.com/in/kerwindobbs
>
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