[gmx-users] OPLS-AA atom types
Mark.Abraham at anu.edu.au
Tue Apr 5 15:21:29 CEST 2011
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.
Announcing your GROMACS version is an excellent idea. See
http://www.gromacs.org/Support for good suggestions when asking for free
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.
> --- 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
>> The correspondence between the atom types and bonded types
>> is all contained in ffnonbonded.itp.
>>> 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.
>> -- ========================================
>> 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
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