On 6/04/2011 1:00 AM, Austin B. Yongye wrote:
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.
Yes, but you're making it hard to help you by forcing us to guess what
content you're looking at. Our time is valuable, and you're not making
it easy for us to give the minimum amount :-) Tell us what file you
looked at, what you saw (copy and paste), and why it's not useful.
Mark
But thanks for your responses anyway.
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, 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<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
========================================
-- gmx-users mailing list gmx-users@gromacs.org
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Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
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Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- ========================================
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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