Hi Raman --
I am unsure why you expect the RNA molecule to be neutral at pH 7. Can you please clarify your reasoning for this? I would expect a negative charge and potential at this pH.
Pacific Northwest National Laboratory
From: Raman Parkesh <rparkesh@...<mailto:rparkesh@...>>
Date: Thu, 23 Dec 2010 13:58:59 -0800
To: APBS List <apbs-users@...<mailto:apbs-users@...>>
Cc: Nathan Baker <nathan.baker@...<mailto:nathan.baker@...>>
I was directed to you by Mr. Yong. I am interested in surface potential analysis of RNA molecule. The problem I have is that I have generated the pqr file of RNA molecule (structure attached) and I think default is pka 7 and then when I run the APBS, it works fine and I get the map file (dx format). When I load it to visualize the electrostatic potential (surface potential) I just get the negative potential. I tried 3-4 times but same thing. I tried this several time through the new webserver but same thing is happening I checked the pqr file and it has still negative charge of -36.00. When I generate pqr file at pKa 7 shouldn't it be the neutral. Do I have to specify something. Also When I run PB calculations that should take care of the phosphate negative charge?
I think I am doing something wrong but I don't know what is wrong. I have attached the pqr file , apbs input (as txt as gmail was not taking extension .in) , pdb of the original structure and the map (dx) file for your reference.
Your response/suggestion will be highly appreciated.