From: Justin A. Lemkul <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] gromos parameterisation in OPLS
To: [EMAIL PROTECTED], "Gromacs Users' List" <gmx-users@gromacs.org>
Date: Tuesday, 17 June, 2008, 4:00 PM
If you include in the .itp file all the necessary
combinations in those
sections, then yes, the .itp file is reasonable and will
use the OPLS-AA
parameters for those specified items. Take care to get the
numbering
right after that point, because you will likely be
inserting lots of
hydrogens!
-Justin
ANINDITA GAYEN wrote:
Sir,
If i insert the hydrogen atoms in the first section of
the itp file, where atomnames , atomtypes , nr, cgnr are
displayed, wil it be wrong. Also, i was talking that, will
the inclusion of "ffoplsaa.itp" will serve the
bonded and nonbonded parameters if i supply the
connectivities in all the bonds, pairs, angles and dihedral
section by the atom numbers?
Thanks for the requested answers.
anindita
--- On Mon, 16/6/08, Justin A. Lemkul
<[EMAIL PROTECTED]> wrote:
From: Justin A. Lemkul <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] gromos parameterisation
in OPLS
To: [EMAIL PROTECTED], "Discussion
list for GROMACS users" <gmx-users@gromacs.org>
Date: Monday, 16 June, 2008, 9:29 PM
Changing the atomtypes will only work if you have
explicit
inclusion of
all hydrogens in your PRODRG-generated topology.
Since the
PRODRG
server outputs a GROMOS-based .itp file, this is
unlikely
unless your
molecule contains only polar or aromatic groups.
If
we're still talking
about CHAPS or cholesterol, this will not be the
case. You
will have
nonpolar groups that, within GROMOS, are atomtype
CH1, CH2,
etc., but
OPLS will not have these UA representations.
I'm not sure what you mean in the last
sentence.
Nothing in this
process will be automatically generated for you.
You're building your
topology by hand. Inclusion of
"ffoplsaa.itp"
will tell grompp which
parameters (bonded and nonbonded) apply to your
molecule.
Calling
"ffoplsaa.itp" will not tell any Gromacs
program
to automatically detect
and generate bonds, dihedrals, etc.
The only way to have "automatic"
generation of
these parameters is to
build an .rtp entry for your molecule that
contains all of
this
information as well, and process your structure
with
pdb2gmx. This is
just as much work as building the topology
yourself, I
think.
-Justin
ANINDITA GAYEN wrote:
Hi,
I came to know from the mailing list that if i
only
change the atomtype in the output itp file of
PRODRG2 and
put the charges as optimised by Gaussian; provided
i
include #include ffoplsaa.itp in the .top file of
the new
molecule and just keep the atom mumbers in
[bonds],
[pairs], [angles] and [dihedrals] as found in the
the all
atom pdb of PRODRG2, the resultant top file will
be a top
file in OPLS format. It was also stated there in
the
mailing list that for the atom numbers mentioned
the opls
staff will put the parameter values necccesary for
the
[bonds], [angles] etc.
Is the approach right?
From Chandigarh to Chennai - find
friends all
over India. Go to
http://in.promos.yahoo.com/groups/citygroups/
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
