Fw: [gmx-users] Amidated C-terminal

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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