Fw: [gmx-users] Amidated C-terminal

Shima Arasteh shima_arasteh2001 at yahoo.com
Thu Jan 3 12:28:07 CET 2013

Thanks for your kind reply.
Maybe I made a mistake unintentionally in modification of files. The CT2 in charmm folder I downloaded from the source, is the same as you wrote.


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Thursday, January 3, 2013 2:47 PM
Subject: Re: Fw: [gmx-users] Amidated C-terminal

On 1/3/13 6:11 AM, Shima Arasteh wrote:
> Have a look at CT2 in aminoacids.c.tdb please:
> [ CT2 ]
> [ replace ]
>   O        CC        12.011    0.55
>   O        O        15.9994    -0.55
> It is +0.55 as what you said. But I see all carbonyl C in aminoacids.rtp file have +0.51 charge.
> I think the amidated C-terminal in my top file should be charged +0.55 as what I see in c.tdb. Shouldn't be? Why it couldn't understand to take +0.55 charge for this last residue?

There is an error in the .tdb file.  The first [replace] line attempts to replace an O atom and assign it a CC type with charge of +0.55, which is then overridden by the next line, which assigns the O atom an O type with -0.55 charge.  The carbonyl C is (erroneously) not adjusted.  The correct line is present in the charmm27.ff folder:

[ CT2 ]
[ replace ]
C      CC      12.011  0.55
O      O       15.9994 -0.55


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

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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