[gmx-users] OPLS-AA atom types

[Austin B. Yongye]

Thanks Justin.
It still doesn't solve my problem, e.g., there are several instances of CT with diferent opls_??? numbers, but no indication of their environments; they could represent C bonded to 1->4 carbon atoms, etc. There's no way of telling. I contacted one of the opls folks last week, but got no response. So I thought I could enlist the help of gromacs users.
But thanks for your responses anyway.
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, 7:32 AM
> 
> 
> Austin B. Yongye wrote:
> > 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.
> 
> You don't need it.  The corresponding file in 4.0.2 is
> called ffoplsaanb.itp. Newer Gromacs versions have a
> different directory and naming structure, but the contents
> of these files is the same.
> 
> Be aware that there have been dozens (if not hundreds) of
> usability upgrades, bug fixes, and new features that have
> been added since 4.0.2.  You would be well-served to
> try to figure out why you can't download a newer version.
> 
> -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, 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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> 
> -- ========================================
> 
> 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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