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Hi,<br>
<br>
The PARSE parameters were developed in order to reproduce the hydration
free energies in PB calculations, while charges taken from different FF
are parametrised by MD or MC. Therefore, I tend to use both the VdW
radii and the charges taken from PARSE. However, check the literature -
many people have used FF parameters in their calculations.<br>
<br>
Ran.<br>
<br>
Marco Ceruso wrote:<br>
<blockquote type="cite"
cite="mid20041010211711.SNB1210.out007.verizon.net@cuauhnahuac">
<pre wrap="">Hi;
If you use Delphi use the PARSE vdw radii set (J. Phys. Chem. 98, 1978-1988
(1994)). For the charges you can keep the OPLS-AA charges.
Marco
</pre>
<blockquote type="cite">
<pre wrap="">-----Original Message-----
From: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>
[<a class="moz-txt-link-freetext" href="mailto:gmx-users-bounces@gromacs.org">mailto:gmx-users-bounces@gromacs.org</a>] On Behalf Of Marc Baaden
Sent: Sunday, October 10, 2004 4:49 PM
To: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
Subject: [gmx-users] Parameters for PB calculation with
Delphi from Gromacs data
Hi,
I am currently carrying out some Poisson-Boltzmann
calculations with Delphi, on the basis of MD snapshots
obtained with Gromacs. I wonder what parameter set (charges &
radii) would be appropriate for Delphi.
Should one "simply" take the precise charges as used in the
MD simulation, and eventually the VDW-parameter derived
atomic radii, or is there some other magic involved to obtain
reasonable results ?
What are people's experience, and would users be willing to
share their favorite parameter set ?
In particular I wonder whether one would need to have
different specific Delphi parameters depening on the
forcefield used (ffgmx vs ffG43xx vs
oplsaa) ?
Or maybe it is more appropriate to use MEAD, as some Gromacs
tools allow to write corresponding input structures ?
Any clarification or (Gromacs related/specific) litterature
reference is welcome.
Thanks in advance,
Marc
--
Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris
<a class="moz-txt-link-freetext" href="mailto:baaden@smplinux.de">mailto:baaden@smplinux.de</a> - <a class="moz-txt-link-freetext" href="http://www.marc-baaden.de">http://www.marc-baaden.de</a>
FAX: +49 697912 39550 - Tel: +33 15841 5176 ou +33 609 843217
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</pre>
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</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
------------------------------------------------------
Ran Friedman
Laser Laboratory for Fast Reactions in Biology
Department of Biochemistry
Faculty of Life Sciences
Tel-Aviv University
Tel. +972-3-6409824
Fax. +972-3-6409875
------------------------------------------------------
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