Re: [PyMOL] Charged Surface Calculation at different pHs?

[Soisson, S. M <ste...@me...>]

Thanks Carsten and David Hall - I'll get started there.
 
Thanks again!
 
Steve

________________________________

From: Schubert, Carsten [PRDUS] [mailto:CSC...@it...] 
Sent: Wednesday, April 07, 2010 2:22 PM
To: Soisson, Stephen M; pym...@li...
Subject: RE: [PyMOL] Charged Surface Calculation at different pHs?



Steve,

 

you need to use PDB2PQR to generate your pqr file, with choice of pH and
then run APBS on that file. I pulled reasonable defaults for APBS from
the APBS plugin tool. PDB2PQR is accessible through the APBS website. 

 

 

HTH

 

                Carsten

 

 

From: Soisson, Stephen M [mailto:ste...@me...] 
Sent: Wednesday, April 07, 2010 12:49 PM
To: pym...@li...
Subject: [PyMOL] Charged Surface Calculation at different pHs?

 

Hi- 

Does anyone know if it is possible to calculate the charged surface
using apbs at different pHs?  I am assuming the default pH is 7.

Thanks in advance- 

Steve 

 

Notice:  This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates Direct contact information
for affiliates is available at
http://www.merck.com/contact/contacts.html) that may be confidential,
proprietary copyrighted and/or legally privileged. It is intended solely
for the use of the individual or entity named on this message. If you
are not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from
your system.
Notice:  This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.