I'd like to estimate binding energies for
several configurations of a ensemble of
structures. Is there a way of reading
multiple pqr files from the same apbs
file? Any help will be greatly appreciated :)
Thereza A. Soares
Pacific Northwest National Lab.
Computational BioSciences Group
P.O. Box 999, K7-90
Richland, WA 99352 - USA
Hi Thereza -
I think what you're asking is if you can include several pqr files in
a single APBS file (if not, please correct me) - if that is the case,
the answer is yes.
For example, please see the protein ligand binding example input from
the APBS Tutorial:
Example input file at: http://apbs.sourceforge.net/doc/tutorial/x267.html
Some things to note:
* The PQR files are listed sequentially in the "READ" section, and the
ordering is important to note since each elec statement needs to use
the "mol" keyword to identify which PQR file to use. This is also in
the example file.
* If you still want to center about each PQR file for each ELEC
statement, you'll need to make sure you use, for example, "fgcent mol
2" to tell APBS which PQR file you want to center on.
Let me know if you have any further questions -
On 4/21/06, Thereza Soares <tasoares@...> wrote:
> hello all,
> I'd like to estimate binding energies for
> several configurations of a ensemble of
> structures. Is there a way of reading
> multiple pqr files from the same apbs
> file? Any help will be greatly appreciated :)
> Thereza A. Soares
> Research Scientist
> Pacific Northwest National Lab.
> Computational BioSciences Group
> P.O. Box 999, K7-90
> Richland, WA 99352 - USA
> Phone: 509.372.6785
> Fax: 509.375.4720
> web: http://www.emsl.pnl.gov/docs/cbbb/index.html
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