Re: [Apbs-users] Question about setting up the electrostatic potential calculation

[Nathan B. <ba...@bi...>]

Hi Sing --

It makes sense. But I have two questions. First of all, since the ligand is
> covalently bounded to the protein and I don't have the parameter of the
> ligand and also I am unable to generate the pqr file based on the crystal
> structure that contains have the ligand.
>

However, you're only interested in its influence on the dielectric function
so you don't need detailed parameters -- just radii which are large enough
to exclude solvent from the binding cavity, right?


> As the same time could you show me what you just taught me in the below
> message?
>

The PQR format is described here:
http://apbs.wustl.edu/MediaWiki/index.php/PQR_format

It's basically a modified PDB format.  You can manually edit the radius
column to alter the radii of these atoms.


> Secondly, if I use the method you just showed me, am I be able to see the
> electrostatic potential map of the binding pocket?  would if be consider the
> ligand is part of the binding pocket so I can't see the map just for the
> binding pocket?
>

You could generate the electrostatic potential using the modified PQR and
then visualize the result using the original PDB file.

-- Nathan


> Thank you very much for your kindly reply
>
> Sing
>
> On Dec 31, 2008, at 9:40 AM, Nathan Baker wrote:
>
> Hello --
>
> I think I understand now:  you would like the binding cavity to be
> solvent-excluded so you can mimic the effect of the ligand being present.
> If this is the only reason why you'd like the cavity to be solvent excluded,
> then why not just put several large-radius zero-charge dummy atoms in the
> binding site to exclude it from solvent?  You could even use the original
> ligand geometry (just assigning very large radii to the atoms and turning
> off the charges) to help you with this process.
>
> Thanks,
>
> Nathan
>
> On Tue, Dec 30, 2008 at 10:56 AM, Kin Sing Stephen Lee <
> si...@ch...> wrote:
>
>> Dear Nathan,
>> In my case, it is a little bit different because my ligand is covalently
>> bonded with the protein and I don't have the parameter of the ligand so I
>> just delete the ligand from the crystal structure so I don't know how to set
>> up the apbs calculation with thise case. But the binding pocket should not
>> be solvent exposed.
>>
>> Thank you
>>
>> Sing
>>
>> On Dec 30, 2008, at 11:39 AM, Nathan Baker wrote:
>>
>> Hi Sing --
>>
>> Have you checked to see whether this binding cavity is solvent exposed?
>> For example, have you used "write dx dielx..." or similar (see
>> http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#write)
>> in an APBS calculation and visualized the resulting map to see if this
>> region of the molecule is really solvent exposed in the APBS calculation?
>>
>> Thanks,
>>
>> Nathan
>>
>> On Mon, Dec 29, 2008 at 7:54 PM, Kin Sing Stephen Lee <
>> si...@ch...> wrote:
>>
>>> Dear all,
>>>
>>> I have a question about out the parameter of apbs regarding the
>>> electrostatic potential calculation.
>>>
>>> I am trying to calculate the electrostatic potential of the binding
>>> pocket. The binding pocket is very hydrophobic and almost totally
>>> embedded inside the protein. So the question is when I set up the
>>> APBS calculation should I still consider the binding pocket have the
>>> dielectric constant of 80 or 2?
>>> If I should set it at 2 is there any possible way that I can restrict
>>> the binding pocket has a dielectric constant of 2 but outside the
>>> protein is 80?
>>>
>>> Thank you very much
>>>
>>> Sing
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
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>>
>>
>>
>> --
>> Associate Professor, Dept. of Biochemistry and Molecular Biophysics
>> Center for Computational Biology, Washington University in St. Louis
>> Web: http://cholla.wustl.edu/
>>
>>
>>
>
>
> --
> Associate Professor, Dept. of Biochemistry and Molecular Biophysics
> Center for Computational Biology, Washington University in St. Louis
> Web: http://cholla.wustl.edu/
>
>
>


-- 
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/