I also continually had this problem unless I got pqr coordinates
(with hydrogens)
below is the instructions I wrote for myself and group so that I
would be able to do it again next time (getting old and the memory
isn't what it used to be)
pqr corrdinates - Can do it on the web at
http://pdb2pqr.sourceforge.net/
http://agave.wustl.edu/pdb2pqr/server.html
I just used the defaults
Under plugins go to APBS tools
Choose use another PQR. (maybe if you select Use PDB2PQR it might do
this automatically without first going on line to do it?)
default configuration
Each time I’ve always had to set the APBS binary location. The other
sections leave blank
default Temporary File Locations
To start APBS 1st select Set Grid, then do Run APBS – I don’t know
why the buttons are placed in that order. Also, it seems you must
click on Run APBS twice before it launches. Run Top in unix window
to make sure it runs
For Hfq, ~400 residues, APBS took about a minute.
Go to Visualization and click on Update
For most reasonable looking Molecular Surfaces I turn off Solvent
Accessible Surface and turn on Color by potential on sol. acc. surf.
Select Show. If you change the range you must also click on Update
When I tried to do this with another loaded structure, it actually
looked like it mapped the first EPS onto the surface of the second
structure.
Make sure to remove waters (and probably everyother non-protein
residue). EP on the left was done with waters in structure. Notice
red surface where ever water molecules appeare
non-linear Bolzman
Linear Bolzman
On May 24, 2007, at 1:16 PM, Michael Lerner wrote:
Hi,
Can you try installing the most recent version of my plugin from
http://www-personal.umich.edu/~mlerner/Pymol/index.html (you can use
the normal Install Plugin menu option .. there's no need to do things
by hand anymore)? It fixes some problems and gives better error
messages on others.
Thanks,
-Michael
--
Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner
On 5/24/07, Oganesyan, Vaheh <oganesy...@medimmune.com> wrote:
I'll appreciate some help with APBS plugin.
In both Win or Lin the same error appears:
ObjectMapLoadDXFile-Error: Unable to open file!
After googling with this error message I've checked all of the
possibilities:
Map file is loaded OK, folders with apbs.exe and psize.py files do
not
contain blanks,
the *.pqr file is created using pdb2pqr server with and without chain
identifier.
At this point I do not know what else to try. Before (about 1 year
ago) I've
used it with no problems.
Could someone point me to the problem?
Windows version is 0_99rc6 installed using binaries.
Thanks in advance.
Vaheh Oganesyan
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