[gmx-users] OPLS-AA atom types

[Austin B. Yongye]

Justin:
I am using gromacs version 4.0.2. Several attempts to download current gromacs versions from http://www.gromacs.org/Downloads kept yielding 93.0-byte files. So I re-installed my pre-existing v4.0.2 without any problems (>./configure --enable-sse; make; make install).
If you could send me the ffnonbonded.itp file that would be great.
Austin-

--- 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, 6:06 AM
> 
> 
> Austin B. Yongye wrote:
> > Thanks Justin.
> > Could you/someone please forward the file? I don't
> have it.
> 
> It's part of your Gromacs installation. 
> $GMXLIB/oplsaa.ff/ffnonbonded.itp.
> 
> If you don't have it, then Gromacs wasn't properly
> installed and you won't be 
> able to use whatever force field for which you're designing
> your topologies.
> 
> -Justin
> 
> > Austin-
> > 
> > --- 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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> 
> -- 
> ========================================
> 
> 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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