VMD-L Mailing List

From: wolfinbm_at_uci.edu
Date: Wed Dec 27 2006 - 11:34:11 CST

Hello
I finally got a working file of PETE, unfortunately, I have pretty much no
idea how to combine the PETE fragment into a large polymer (or even into a
PETE dimer, for that matter). My immediate goal is to be able to put the
PETE fragments together to produce a polymer. Then I want to make the
first layer of the membrane with a hole in the middle. Finally, I will
want to make many layers with an appropriate sized hole in each layer to
create a membrane with a conical pore. Any advice on where to start here?

Thanks & Best,
Matt

> Hi Matt,
> Molefacture (and, for that matter, all plugins) does not yet save its
> state along with th rest of the VMD save state function. It's something
> we are currently working on, but it is difficult to combine the
> modularity (and variety of origins) of the plugins with the machinery
> necessary for a true save state. In the meantime, though, you should be
> able to just save your molecule as an XBGF (using the molefacture file
> menu) and load it again to restore your place, since molefacture's
> internal state is almost all calculated on the fly from the molecule
> being worked on.
> Peter
>
> wolfinbm_at_uci.edu wrote:
>> Hello
>> The problem I had was fixed; however, I am having a problem saving my
>> work. I can use the "save state" function in VMD, but when I re-load
>> it,
>> nothing displays (even though the "D" button is on). Any suggestions?
>>
>> Thanks & Best,
>> Matt Wolfinbarger
>>
>>
>>> Hello
>>> Thank You--the new version seems to work. But I've still got a long
>>> way
>>> to go on building the membrane...
>>>
>>
>>
>>> Thanks & Best,
>>> Matt Wolfinbarger
>>>
>>
>>
>>> Ah yes, the infamous spaces-in-filenames issue; this had been causing
>>>
>> problems on windows. This bug should have been fixed in the 1.8.5 plugin
>> update -- did you download a fresh copy of the 1.8.5 installer? If so,
>> please try the 1.8.6 alpha instead
>>
>>> (http://www.ks.uiuc.edu/Research/vmd/alpha/). Please let me know if you
>>>
>> still have problems.
>>
>>> Peter
>>>
>>> wolfinbm_at_uci.edu wrote:
>>>
>>>> Hello
>>>>
>>>>
>>>>
>>>>> Hi Matt,
>>>>> two notes:
>>>>> -which version of vmd are you using? I'm somewhat puzzled by these
>>>>> error
>>>>>
>>>>>
>>>> messages...
>>>>
>>>>
>>>>
>>>>> I'm using version 1.8.5. Maybe the program, or at least the
>>>>> molefacture
>>>>> plugin, did not install correctly. I will try uninstalling VMD,
>>>>>
>>>>>
>>>> download >whatever that latest version is available, and re-install.
>>>>
>> If that >doesn't work I'll send another message to the list and give
>> more
>>
>>>>> specifics on the error message.
>>>>>
>>>>>
>>>> I tried re-installing and I am still getting the error message. When
>>>> I go
>>>> to the menu function "Build" in molefacture, I use the menu function
>>>> "new
>>>> molecule from fragment." Here is the details of the error message:
>>>>
>>>> (BEGIN)
>>>> wrong # args: should be "::Molefacture::new_mol_from_fragment
>>>> fragpath"
>>>>
>> wrong # args: should be "::Molefacture::new_mol_from_fragment fragpath"
>> while executing
>>
>>>> "::Molefacture::new_mol_from_fragment C:/Program Files/University of
>>>>
>> Illinois/VMD/plugins/noarch/tcl/molefacture1.1/lib/basemol/benzene.mfrag"
>>
>>>> (menu invoke)
>>>> (END)
>>>>
>>>> Note that this applies for any fragment--benzene is just the one I
>>>>
>> happened to pick this time.
>>
>>>> Thank You,
>>>> Matt
>>>>
>>>>
>>>>
>>>>
>>
>>
>>
>>
>