[gmx-users] oplsaa galactose

[Justin A. Lemkul]

nishap.patel at utoronto.ca wrote:
> Hello,
> 
>     I am trying to simulate hexopyronase using OPLS-AA forcefield using 
> parameters from the paper:
> 
> An improved OPLS?AA force field for carbohydrates, 2002 by Gunsteren.
> 
> I was looking through the ffoplsaabon.itp file and there are some 
> dihedral parameters for hexopyronase. I am not sure what the comment 
> below means.
> 
>   Below are extra dihedrals for some special organic molecules.
> ; Since the atom types are identical to other dihedrals you have to specify
> ; them explicitly with a define if you happen to simulate this type of 
> molecule.
> 
> How would I mention it in my rtp file? I don't understand ' specify
> them explicitly with a define'  This is my .rtp for Galactose
> 

See examples in aminoacids.rtp, e.g. ARG.

-Justin

> [ GLA ]
>  [ atoms ]
>      O    opls_180   -0.400     1
>     C1       opls_195    0.365     2
>     H1    opls_196    0.100     2
>     O1    opls_154   -0.683     2
>     HO1   opls_155    0.418     2
>     C2       opls_158    0.205     3
>     H2    opls_176    0.060     3
>     O2    opls_154   -0.683     3
>     HO2   opls_155    0.418     3
>     C3       opls_158    0.205     4
>     H3    opls_176    0.060     4
>     O3    opls_154   -0.683     4
>     HO3   opls_155    0.418     4
>     C4       opls_158    0.205     5
>     H4    opls_176    0.060     5
>     O4    opls_154   -0.683     5
>     HO4   opls_155    0.418     5
>     C5       opls_183    0.170     6
>     H5    opls_185    0.030     6
>     C6    opls_157    0.145     7
>     H61   opls_176    0.060     7
>     H62   opls_176    0.060     7
>     O6    opls_154   -0.683     7
>     HO6   opls_155    0.418     7
>  [ bonds ]
>      O    C1
>      C1   H1
>      C1   O1
>      O1   HO1
>      C1   C2
>      C2   H2
>      C2   O2
>      O2   HO2
>      C2   C3
>      C3   H3
>      C3   O3
>      O3   HO3
>      C3   C4
>      C4   H4
>      C4   O4
>      O4   HO4
>      C4   C5
>      C5   C6
>      C5   O
>      C6   H61
>      C6   H62
>      C6   O6
>      O6   HO6
> 
> 
> 
> 

-- 
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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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