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 <jalem...@vt.edu> wrote:
From: Justin A. Lemkul <jalem...@vt.edu>
Subject: Re: [gmx-users] OPLS-AA atom types
To: "Discussion list for GROMACS users" <gmx-users@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 <jalem...@vt.edu>
wrote:
From: Justin A. Lemkul <jalem...@vt.edu>
Subject: Re: [gmx-users] OPLS-AA atom types
To: "Discussion list for GROMACS users" <gmx-users@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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