Hi Gokul –

 

I would try it and see.  Be sure to use the “write atompot” command.

__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  509-375-3997

http://kdi.pnnl.gov/bios/baker.stm

 

From: gokul vasudev [mailto:vasudevg@uwindsor.ca]
Sent: Tuesday, May 31, 2011 9:35 AM
To: Keith Callenberg
Cc: apbs-users@lists.sourceforge.net
Subject: Re: [Apbs-users] electrostatic potential issue

 

Hey Keith

 

Thanks for your reply.

I really appreciate your help.

 

I need to know 1 thing.If suppose i have a 2MTA pdb with chains A and H interacting with each other.

 

Now if i run APBS individually with only chain A  and then only with chain H .

 

and finally keeping both chains A and H. and run apbs with command calc energy comps.

 

Will apbs now show the value of elctrostatic energy per atom for both chains(A and H) in combination or will it still show individually for A and H?

 

 

thanks and regards

gokul

 

 

 



 

On Thu, May 26, 2011 at 11:30 AM, Keith Callenberg <kmc112@pitt.edu> wrote:

Hi Gokul,

I'm not sure if this is what you're interested in, but if you use
"calcenergy comps" instead of "calcenergy total" APBS will provide the

per-atom electrostatic energy components. Maybe you'd have to manually
turn off other charges to isolate pairs if that is what you're
interested in? I'm not sure if there's an easier way.


http://www.poissonboltzmann.org/apbs/user-guide/running-apbs/input-files/elec-input-file-section/elec-keywords/calcenergy

Keith

--
Keith M. Callenberg
Carnegie Mellon-University of Pittsburgh Program in Computational Biology
kmc112@{pitt,cmu}.edu
http://www.pitt.edu/~kmc112/

On Thu, May 26, 2011 at 12:16 AM, gokul vasudev <gokul472@gmail.com> wrote:

> Hi
>
> I am trying to find electrostatic potential values of pairs of atoms at
> interface (protein - protein interaction).
>
> Could anyone please guide me how do i compute these electrostatic potential
> values for pair of atoms/amino acids?
> Can APBS help me out (as i understand it gives electrostatic potential
> values for protein-solvent interaction)
>
>
> Looking forward for a positive response.
>
> Thanks and regards
> Gokul
> Univ of Windsor
>
>

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