[gmx-users] Parameters for PB calculation with Delphi from Gromacsdata

[Marco Ceruso]

Hi,
 
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_elec term that comes from your FF
electrostatic representation.
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. 
Hope this helps
Marco
 



  _____  

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Ran Friedman
Sent: Monday, October 11, 2004 9:46 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Parameters for PB calculation with Delphi from
Gromacsdata


Hi,

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.

Ran.

Marco Ceruso wrote:


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  

  

-----Original Message-----

From: gmx-users-bounces at gromacs.org 

[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Marc Baaden

Sent: Sunday, October 10, 2004 4:49 PM

To: gmx-users at gromacs.org

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

 mailto:baaden at smplinux.de      -      http://www.marc-baaden.de

 FAX: +49 697912 39550  -  Tel: +33 15841 5176 ou +33 609 843217





_______________________________________________

gmx-users mailing list

gmx-users at gromacs.org

http://www.gromacs.org/mailman/listinfo/gmx-users

Please don't post (un)subscribe requests to the list. Use the 

www interface or send it to gmx-users-request at gromacs.org.



    



_______________________________________________

gmx-users mailing list

gmx-users at gromacs.org

http://www.gromacs.org/mailman/listinfo/gmx-users

Please don't post (un)subscribe requests to the list. Use the 

www interface or send it to gmx-users-request at gromacs.org.

 

 +++++++++++++++++++++++++++++++++++++++++++

 This Mail Was Scanned By Mail-seCure System

 at the Tel-Aviv University CC.

  


-- 

------------------------------------------------------

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

------------------------------------------------------

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20041011/cd5bc10b/attachment.html>