[gmx-users] oplsaa galactose

[nishap.patel at utoronto.ca]

Hi,

   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.

The set of torsional angle parameters in the paper are given in  
Kcal/mol, but because I am using OPLS-AA I would need to convert the  
functions into RB-types, right?

Is there a way to convert these functions to RB-types? Or do I convert  
them from Kcal/mol to KJ/mol?

Thanks.

Nisha P



Quoting 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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