Fw: [gmx-users] Amidated C-terminal
jalemkul at vt.edu
Thu Jan 3 12:17:50 CET 2013
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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