[gmx-users] Question about the dihedrals in top file using OPLS force field in GROMACS

[Justin A. Lemkul]

Yanmei Song wrote:
> Hi,Justin:
> 
> Thanks for your response.
> 
> I have read that part and still confused. Does it mean that if I
> choose the ffoplsaa.itp in my top, I used the RB potential for
> Dihedrals or the periodic type? Also actually I can only get the
> parameters for phi, cp and mult (listed above) Can I use these
> parameters directly for my itp user ffoplsaa force field? Thanks a
> lot!
> 

OPLS does use the R-B potential.  It looks like that topology is a PRODRG 
product, in which case, no, your topology is not suitable for use with OPLS. 
PRODRG generates Gromos-type topologies.

-Justin

> 2009/1/28 Justin A. Lemkul <jalemkul at vt.edu>:
>>
>> Yanmei Song wrote:
>>> Hi,
>>>
>>> I am using ffoplsaa.itp as my force field to do a simulation using
>>> GROMACS.
>>> I have a question about how to write the parameters in dihedrals in
>>> the itp file.
>>>
>>> [ dihedrals ]
>>> ; ai  aj  ak  al  fu    c0, c1, m, ...
>>>   1   2   5   6   1    0.0    3.77   3    0.0    3.77   3 ; dih   CAA
>>>  CBF  OAW  CBH
>>>   2   5   6   9   1    0.0    3.77   3    0.0    3.77   3 ; dih   CBF
>>>  OAW  CBH  OAY
>>>   5   6   9  10   1    0.0    3.77   3    0.0    3.77   3 ; dih   OAW
>>>  CBH  OAY  CBJ
>>>   6   9  10  13   1    0.0    3.77   3    0.0    3.77   3 ; dih   CBH
>>>  OAY  CBJ  OBA
>>>   9  10  13  14   1    0.0    3.77   3    0.0    3.77   3 ; dih   OAY
>>>  CBJ  OBA  CBL
>>>
>>> Then if I am choosing ffoplsaa.itp force field, what is the meaning
>>> for c0,c1 and m under the [dihedrals]? Since i know that GROMOS and
>>> OPLS force field have a different format for proper dihedrals. For
>>> OPLS it seems there are four other parameter like v1 v2 v3 v4. Then my
>>> question is how can i define the dihedral parameters in itp file based
>>> on ffoplsaa force field in GROMACS? Thanks a lot!
>>>
>> Refer to the manual, section 4.2.12 "Proper Dihedrals."
>>
>> -Justin
>>
>>> Yanmei
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> 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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> 
> 
> 

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================