Re: vmd-l: Membrane builder ?'s

From: Christopher Hartshorn (cmhartshorn_at_wsu.edu)
Date: Tue Feb 24 2009 - 00:47:57 CST

On Feb 23, 2009, at 10:06 PM, John Stone wrote:

John,

Thanks. Ill look him up. As far as VMD, I did have alpha 30
(6202008) before this one, and I did not experience the same abnormal
quitting. Like I said it does not serve as a problem as far as I can
tell, with the exception of having to click "Ok" to close the Error
box that pops up when I quit. But I figured it was worth a mention
just in case it represented some larger issue, which I can not see on
my end.

Best,
Chris

>
> Hi,
>
> On Mon, Feb 23, 2009 at 11:09:16AM -0800, Christopher Hartshorn wrote:
>> Hello everyone.
>> I have been looking at the membrane builder plugin and still have a
>> question about the membranes generated, after reading the online
>> info. In regards to the "pre-equilibriated" patch, how long was it
>> "pre-equilibriated" before being put into this plugin? Also, is
>> there
>> a new version with more lipid types (e.g beyond POPE and POPC)?
>
> Regarding the equilibrated patch, the person to ask is Ilya Balabin
> who is the original developer of the plugin. He's at Duke now, and
> his web page is here: http://www.chem.duke.edu/~ilya/
>
>> Finally, on a different note, I have been using the latest VMD alpha
>> build (VMD 1.8.7 a51 Mac OSX) and there is a minor (and I mean
>> MINOR)
>> problem when quitting the program. The program spits out the
>> following error message every time I quit the program:
>> ERROR
>> while executing
>> "exit"
>> After I click Ok to the message, the program quits itself anyway,
>> effectively eliminating this from being an actual problem. But I
>> felt
>> I should mention it anyway.
>
> Interesting. Had you tested any of the older alpha versions, and did
> you ever see this before? Or has this only occured with a51? I'd
> been
> working through a few unusual bugs that cropped up with the
> migration to
> Tcl/Tk 8.5.x, so this may be related to one of the ones I've already
> fixed,
> but we can verify this by having you test a newer test build when I
> post
> one in a day or two.
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>>
>> Thank you for any and all replies.
>>
>> Chris Hartshorn
>> WSU
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078

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