[gmx-users] oplsaa galactose

[nishap.patel at utoronto.ca]

Thanks Justin!


Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

>
>
> 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
>>
>>
>>
>>
>
> -- 
> ========================================
>
> 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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