Hi Tomek –

 

Sorry; I misunderstood your question.

 

Can you please share examples of the output you are trying to merge?

 

Thanks,

 

--

Nathan Baker

Laboratory Fellow and Technical Group Manager

Applied Statistics and Computational Modeling

Pacific Northwest National Laboratory

+1-509-375-3997

http://www.linkedin.com/in/nathanandrewbaker/

 

From: Tomek Wlodarski [mailto:tomek.wlodarski@gmail.com]
Sent: Wednesday, February 19, 2014 7:08 AM
To: apbs-users@googlegroups.com
Cc: Tomek Wlodarski; apbs-users@lists.sourceforge.net; Baker, Nathan
Subject: Re: [apbs-users] merge atompot flat file

 

Hi Nathan,

 

Thank you for replay.

But mergedx works only with DX file format, is that right? but I have flat files - txt.

I wanted to calculate electrostatic potential per residue but apbs can calculate only for atoms. So I was thinking of calculating for each atom and them sum across each residue - I know that this is not perfect but I have not other idea how to calculate electrostatic potential per residue - to have one number for each residue.

Thanks.

Best,

 

tomek

 

 

W dniu wtorek, 18 lutego 2014 21:51:08 UTC użytkownik Baker, Nathan napisał:

Hi Tomek –

 

Your first question is straightforward to answer:  you should use the mergedx program that is distributed with APBS (http://www.poissonboltzmann.org/apbs/user-guide/apbs-tools/mergedx2). 

 

For the second question, are you referring to the output files you generate with “write atompot”?  Would you be willing to share some examples?

 

Thanks,

 

--

Nathan Baker

Laboratory Fellow and Technical Group Manager

Applied Statistics and Computational Modeling

Pacific Northwest National Laboratory

+1-509-375-3997

http://www.linkedin.com/in/nathanandrewbaker/

 

From: Tomek Wlodarski [mailto:tomek.w...@gmail.com]
Sent: Monday, February 17, 2014 9:11 AM
To: apbs-...@googlegroups.com
Subject: [apbs-users] merge atompot flat file

 

Hi,

 

I am using atompot flag for my run with 4 cores.

I end up with 4 txt files. My question is how I should merge those files into one?

I noticed that some atoms have non zero value in mor than one file - so should I add this values to get proper electrostatic potential on this atom?

Thanks.

Best,

 

tomek