Michael McGovern wrote:
Hi everyone. I'm doing some simulations involving the sugar trehalose,
with the 53a6 force field. There is an odd issue I am having with the
rtp file for trehalose. It seems to be charged. Here is the beginning
of the rtp entry:
[ TRH ]
[ atoms ]
HO4 H 0.41000 0
O4 OA -0.64200 0
C4 CH1 0.23200 0
C3 CH1 0.23200 1
O3 OA -0.64200 1
HO3 H 0.41000 1
C2 CH1 0.23200 2
O2 OA -0.64200 2
HO2 H 0.41000 2
C6 CH1 0.23200 3
O6 OA -0.64200 3
HO6 H 0.41000 3
C5 CH1 0.37800 4
O5 OA -0.45000 4
C1 CH1 0.24200 4
O1 OA -0.34000 4
C1' CH1 0.24200 4
O5' OA -0.45000 4
C5' CH1 0.37800 4
C4' CH1 0.27500 5
O4' OA -0.60000 5
HO4' H 0.47000 5
C3' CH1 0.23200 6
O3' OA -0.64200 6
HO3' H 0.41000 6
C2' CH1 0.23200 7
O2' OA -0.64200 7
HO2' H 0.41000 7
C6' CH1 0.23200 8
O6' OA -0.64200 8
HO6' H 0.41000 8
Charge group 5 has a net charge of +0.145. Is this a typo? Should I
just change it to be the same as the other C-O-H charge groups?
The net charge certainly seems wrong. Before making any ad hoc changes, though,
refer to the primary literature for the force field and make sure everything
else is right. I think 53a6 has the same charges as 45a4, wherein the sugar
parameters were improved from 45a3. I don't see any mention of modifications to
sugars in the 53a6 paper. 45a4 ref:
Lins and Hunenberger (2005) J Comput Chem 26: 1400-1412.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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