Hello –

 

Can you please provide more information about your calculation; e.g., including the APBS input file and what you mean by a “high” energy?

 

Thanks,

__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  509-375-3997
http://kdi.pnl.gov/bios/baker.stm

 

From: Arnab Nayek [mailto:narnab1983@gmail.com]
Sent: Tuesday, August 30, 2011 9:38 PM
To: apbs-users@lists.sourceforge.net
Subject: [Apbs-users] total electrostatic energy of a native protein can be positive

 

Dear Sir,

            I am interested to do some APBS calculation in my research work. Actually I want to calculate the salt bridge energy of a protein. So for that purpose I follow a model and run the APBS for electrostatic energy calculation. APBS is running well but the energy which it produce is thought to be very high and also the problem is the total electrostatic energy of a native protein, which APBS produce is always positive value. Is it true? I have a confusion about this. Please help me to correct my problem.

 

Thanking you.

 

 

 

Arnab Nayek

PhD scholar (Bioinformatics)

Dept. Of Biotechnology

Burdwan University, WB, India