Chun,

Here is another site to check out. It is Michael Lerner's site, the guy who brings us the APBS PyMol Plugin. He mentions some information about the plugin and also has contact info in case the website doesn't answer your question.

http://www-personal.umich.edu/~mlerner/PyMOL/

At a quick glance, it seems to use AMBER force field. I know that the pdb2pqr server has several parameters for you to choose from, so you might check out the plugin and see how Michael sets those to run within PyMOL. You can check that using any text editor such as Notepad.

Again, hope this helps.



Cheers,
Nick

----- Original Message ----- From: "Noinaj" <noi...@uky.edu>
To: "Chun Tang" <tcsuz...@gmail.com>
Sent: Wednesday, April 12, 2006 10:45 AM
Subject: Re: [PyMOL] pqr file


Chun,

You might check out the web site below, it probably contains all information that you might need and contact information for things not explained online.

http://apbs.sourceforge.net/

Hope this helps.



Cheers,
Nick



----- Original Message ----- From: "Chun Tang" <tcsuz...@gmail.com>
To: <pymol-users@lists.sourceforge.net>
Sent: Tuesday, April 11, 2006 6:39 PM
Subject: [PyMOL] pqr file


Hi there,

When one uses the APBS plugin of pymol to generate a pqr file, how
dose it assign the partial charges to the atoms, what force field is
it based on? Thank you.

Chun


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