Re: [PyMOL] Has anyone got apbs 0.4 to work with the pymol apbs plugin?

[Michael G. L. <ml...@um...>]

On Wed, 21 Dec 2005, William Scott wrote:

>
> Dear Michael:
>
> Thanks.
>
> It works great.  Sorry that I stupidly didn't think to check it.

No problem.  I'm glad it works.  Almost everything should be the same. 
APBS has a new required parameter, sdens (Vacc sphere density) that I've 
added to the configuration pane.  As far as I've heard, the default 
setting of 10.0 should be fine for most uses.

> If you permit me one whine, I still need to use pdb2pqr (new version of 
> that too) in order to do this with nucleic acids.

Allowing the plugin to use pdb2pqr is at the top of my PyMOL-related todo 
list.

-michael

--
www.umich.edu/~mlerner |                        _  |Michael Lerner
This isn't a democracy;| ASCII ribbon campaign ( ) |   Michigan
it's a cheer-ocracy.   |  - against HTML email  X  |  Biophysics
-Torrence,  Bring It On|                       / \ | mlerner@umich

>
>
> On Tue, 20 Dec 2005, Michael George Lerner wrote:
>
>>
>> There's a new version on my website
>> (http://www.umich.edu/~mlerner/PyMOL/).  Please feel free to try it out
>> and let me know if it works.  I've tested it on a few systems that I work
>> with, and it seems fine.  One person has reported some difficulties, but
>> these may not be related to my plugin.
>>
>> Thanks,
>>
>> -michael
>>
>> --
>> www.umich.edu/~mlerner |                        _  |Michael Lerner
>> This isn't a democracy;| ASCII ribbon campaign ( ) |   Michigan
>> it's a cheer-ocracy.   |  - against HTML email  X  |  Biophysics
>> -Torrence,  Bring It On|                       / \ | mlerner@umich
>>
>> On Tue, 20 Dec 2005, William Scott wrote:
>>
>>> I'm not getting very far...
>>>
>>> parsePBE:  Warning -- parsed deprecated "calcforce 0" statement.
>>> parsePBE:  Please use "calcforce no" instead.
>>> PBEparm_check: SDENS not set!
>>> NOsh:  MG parameters not set correctly!
>>> Error while parsing input file.
>>>
>>>
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>>
>
>
>