[gmx-users] OPLS-AA atom types

[Mark Abraham]

On 5/04/2011 11:03 PM, Austin B. Yongye wrote:
> Thanks Justin.
> Could you/someone please forward the file? I don't have it.
> Austin-

Announcing your GROMACS version is an excellent idea. See 
http://www.gromacs.org/Support for good suggestions when asking for free 
help.

Because you haven't, we have to suppose that either your installation is 
broken, you're not looking at it properly, or you're using a version 
before 4.0 that has the information in a file with a different name.

Mark


> --- On Tue, 4/5/11, Justin A. Lemkul<jalemkul at vt.edu>  wrote:
>
>> From: Justin A. Lemkul<jalemkul at vt.edu>
>> Subject: Re: [gmx-users] OPLS-AA atom types
>> To: "Discussion list for GROMACS users"<gmx-users at gromacs.org>
>> Date: Tuesday, April 5, 2011, 5:19 AM
>>
>>
>> Austin B. Yongye wrote:
>>> Hello GROMACS USERS,
>>> Does any one have a document/manual/link that
>> describes the name-number atom type mappings employed in
>> opls-aa?
>> The correspondence between the atom types and bonded types
>> is all contained in ffnonbonded.itp.
>>
>> -Justin
>>
>>> I would like to build some molecules and specify their
>> parameters, but I see different of numbers for the same atom
>> type name, e.g:
>>> TYPE NAME
>>> 135  CT
>>> 136  CT
>>> 137  CT
>>> 157  CT
>>>
>>> I can deduce that 135 is CH3-, 136 is R-CH2-, and 137
>> is RRCH- by looking at topology files.
>>> Thanks,
>>> Austin-
>> -- ========================================
>>
>> 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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