P wrote:
Dear All
I have question for people who use dppc lipids with ffG43a2x.tgz force
field
(GROMOS96 modified to describe lipids). I want to change to newer
GROMOS96
force field (in order to simulate membrane/protein water systems) and
I would
like to make *.itp file for dppc lipid molecule that is in agreement with
ffG43a2x.tgz from the contribution section of gromacs website.
ffG43a2x.tgz force field has two new atoms types LCH3 and LCH2 that can be
used to describe long lipid chains. There are also new LJ parameters for
those atoms in ffG43a2xnb.itp. What is the procedure for obtaining *itp
for dppc molecule that can be used with this force field.
1) Should I use PRODRGbeta for creating dppc.itp topology and
manually change atom types describing lipid long chains CH3 to LCH3
and then CH2 to LCH2.
2) Should I download dppc.itp topology from gromacs benchmark
and manually change the atom types to those present in ffG43a2x.
3) Is there any available software that can be used for
creation of dppc.itp file.
4) .. is there a simpler way?
Please give me some hints and suggestion,
I’m not an expert with gromacs, what is the
right procedure for this.
Thank you for your help.
Best Regards.
Hi P,
there's an alternative way: at
http://moose.bio.ucalgary.ca/index.php?page=Downloads of the group of P.
Tieleman you find a topology and file set for dppc and lipids in
general. Therein, dppc is described as a molecule consisting out of
completely new atom types, but the usability of this set has been proven
in a large amount of publications. Everything else depends on your own
wishes: do you want to simulate a Protein in a membrane: In that case
you'd have to take lipid.itp and exchange all interaction parameters
between lipid- and protein atom types with the ones given in ffG43a2.itp
(e.g. a lipid CH2, named LCH2, interacts with a protein CA exactly like
a protein CH2 with CA). That's a big task and will probably cost you
half a weeks work, but as the Tieleman parameters have been validated,
the resulting parameter set should be a rather reliable one.
cheers
Steffen
--
Dipl.-Chem. Steffen Wolf
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Germany
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