Hello –

 

Yes, there should be a way to do this with “srfm smol” as well.  I would recommend running the calculations for the ligand and receptor with very different values for sdie so it is easy to discriminate the two maps from each other.

 

Thanks,

 

--

Nathan Baker

Laboratory Fellow

Pacific Northwest National Laboratory

+1-509-375-3997

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

 

From: Shun Zhu [mailto:shunz2@uci.edu]
Sent: Thursday, November 07, 2013 10:10 AM
To: Baker, Nathan
Cc: apbs-users@googlegroups.com; APBS-USERS mailing list (apbs-users@lists.sourceforge.net)
Subject: Re: [apbs-users] Using different pdie for the protein and the ligand in the protein-ligand complex?

 

Hi Nathan,

 

  Thanks a lot for the reply! I've tried merging dielectric maps. For example, for the same line in the x-shifted .dx files of the ligand map and the protein map:

 

#For the ligand(pdie=2, sdie=1)

1.000000e+00 2.000000e+00 2.000000e+00

 

#For the protein(pdie=5, sdie=78)

7.800000e+01 7.800000e+01 7.800000e+01

 

Based on my understanding, I just need to do a superposition style of merging. So after merging, the line for the complex should look like the following:

 

7.800000e+01 2.000000e+00 2.000000e+00

 

Does this seem to you the correct way of merging?

 

In addition, the above example has 'srfm' set to mol (I assume this is without smoothing). But with 'srfm' set to smol (smoothed with harmonic averaging), do you know if there is a relatively easy way of doing the merging? Do I need to look into the source code to find the function that was used for the smoothing or there is a better way? Thank you very much!

 

 

Best,

Steve

 

 

 

 

 

 

 

 

 

On Wed, Nov 6, 2013 at 6:16 PM, Baker, Nathan <Nathan.Baker@pnnl.gov> wrote:

Hello –

 

There is no direct way to do this in APBS.  However, you can do it by generating multiple dielectric maps (one for the ligand and one for the protein) and merging them for use in a subsequent calculation.

 

I hope this helps,

 

--

Nathan Baker

Laboratory Fellow

Pacific Northwest National Laboratory

+1-509-375-3997

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

 

From: Steve Zhu [mailto:shunz2@uci.edu]
Sent: Monday, November 04, 2013 2:39 PM
To: apbs-users@googlegroups.com
Subject: [apbs-users] Using different pdie for the protein and the ligand in the protein-ligand complex?

 

Dear APBS users/developers,

 

  I am working on the PB calculations of a protein-ligand complex recently. I wonder if there is an easy way to implement different pdie for the protein and the ligand in the complex calculations, for example, pdie=6 for the protein and pdie=1 for the ligand. Thank you very much!

 

Best,

Steve