are always set to 0 and the barrier heights have sometime a negative
value.
Thank you again for your advice.
SA-
Message: 1
Date: Tue, 19 Jul 2011 11:08:55 -0700 (PDT)
From: Austin B. Yongye ybau...@yahoo.com
Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters
It is normal to have combinations of negative and positive values for the
barrier heights. Those are just the best coefficients to reproduce some QM
rotational energy curve during the parameterization. The negative
periodicities are a convention from AMBER. They simply indicate that the
Hello GROMACS USERS,
Does any one have a document/manual/link that describes the name-number atom
type mappings employed in opls-aa?
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
: 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
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
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
Others alternatives are welcome.
Look up NACCESS. It can do what you want on pdb frames extracted from a
trajectory.
--- On Mon, 12/13/10, Justin A. Lemkul jalem...@vt.edu wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] [Fwd: g_sas for each residu]
To: Discussion
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