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<DIV dir=ltr align=left><SPAN class=691165714-11102004><FONT face=Arial
color=#0000ff size=2>Hi,</FONT></SPAN></DIV>
<DIV><FONT face=Arial color=#0000ff size=2></FONT> </DIV>
<DIV><SPAN class=691165714-11102004><FONT face=Arial color=#0000ff size=2>Ran is
right. One reason to keep the FF charges instead of the PARSE
ones is to be consistent with what was used to generate your
conformation specially when you use the PB calculation results along
with some-type of MMPBSA approach in which you have a
E_</FONT></SPAN><SPAN class=691165714-11102004><FONT face=Arial color=#0000ff
size=2>elec term that comes from your FF electrostatic
representation.</FONT></SPAN></DIV>
<DIV><SPAN class=691165714-11102004><FONT face=Arial color=#0000ff size=2>In our
hands the differences between OPLS-AA and PARSE charges were much less
critical than the differences observed between PARSE radii and the radii
implanted by editconf -mead. </FONT></SPAN></DIV>
<DIV><SPAN class=691165714-11102004><FONT face=Arial color=#0000ff size=2>Hope
this helps</FONT></SPAN></DIV>
<DIV><SPAN class=691165714-11102004><FONT face=Arial color=#0000ff
size=2>Marco</FONT></SPAN></DIV>
<DIV><SPAN class=691165714-11102004><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV><FONT size=2></FONT><BR>
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style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #0000ff 2px solid; MARGIN-RIGHT: 0px">
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<FONT face=Tahoma size=2><B>From:</B> gmx-users-bounces@gromacs.org
[mailto:gmx-users-bounces@gromacs.org] <B>On Behalf Of </B>Ran
Friedman<BR><B>Sent:</B> Monday, October 11, 2004 9:46 AM<BR><B>To:</B>
Discussion list for GROMACS users<BR><B>Subject:</B> Re: [gmx-users]
Parameters for PB calculation with Delphi from
Gromacsdata<BR></FONT><BR></DIV>
<DIV></DIV>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 cite=mid20041010211711.SNB1210.out007.verizon.net@cuauhnahuac
type="cite"><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></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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