[gmx-users] Trehalose RTP file trouble

[Justin A. Lemkul]

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

-- 
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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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