VMD-L Mailing List

From: Charles McCallum (mmccallum_at_pacific.edu)
Date: Tue Oct 25 2005 - 08:19:38 CDT

John, I'm seeing the "autopsf package could not be loaded.." error on
1.8.4a22 under OS X also.

Cheers,

Mike
On Oct 24, 2005, at 3:19 PM, John Stone wrote:

>
> Hi,
> I think the autopsf problem in a22 is a mistake I made in
> building the
> Windows test build. It'll work in the next one I post.
> I don't know anything about the g_hbond/g_dih, or g_sas XML files,
> but I
> do know that VMD doesn't have a plugin to generate those
> currently. You
> may have to create those from the DCD and PSF files either with
> scripts or
> some other method. Perhaps another Gromacs user may have a solution.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Oct 24, 2005 at 04:56:41PM -0500, Armen Nalian wrote:
>
>
>> Yes 1.8.4a22. It gives "The autopsf package could not be loaded:
>> ERROR>
>> Creation of window for 'autopsf' failed."
>>
>> In addition I have a question. I am trying to use gromacs analysis
>> tools,
>> for the dcd trajectory. From vmd I save the trajectory as trr file
>> and it
>> works great, much better than trio.
>> How can I get the tpr tpb tpa xml file I would like to run g_saltbr,
>> g_hbond, g_dih, g_sas.
>> Thank you,
>>
>>
>> Armen Nalian
>>
>>
>>
>> Research Associate
>>
>> E-mail: nalianarmen_at_sfasu.edu
>> Tel: (936) 468-6931
>>
>>
>> Department of Biotechnology
>>
>> Stephen F. Austin State University
>> Science Research Center
>> P.O Box 6132-SFA Station
>> Nacogdoches, Texas 75962-3006
>>
>>
>> -----Original Message-----
>> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On
>> Behalf Of
>> John Stone
>> Sent: Monday, October 24, 2005 1:12 PM
>> To: Armen Nalian
>> Cc: vmd-l_at_ks.uiuc.edu
>> Subject: Re: vmd-l: trouble with autopsf
>>
>>
>> Hi,
>> That's with 1.8.4a22 right? If so, I should have a fix for that
>> shortly.
>>
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Sun, Oct 23, 2005 at 11:36:09PM -0500, Armen Nalian wrote:
>>
>>
>>> I am getting "The autopsf package could not be loaded:" message
>>> on WINXP
>>>
>>> -----Original Message-----
>>> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On
>>> Behalf
>>>
>>>
>> Of
>>
>>
>>> Peter Freddolino
>>> Sent: Saturday, October 22, 2005 5:35 PM
>>> To: rob zehr
>>> Cc: vmd-l_at_ks.uiuc.edu
>>> Subject: Re: vmd-l: trouble with autopsf
>>>
>>> Dear Rob,
>>> VMD version 1.8.3 shipped before the autopsf GUI was completed,
>>> and a
>>> good deal of other work has gone into it since then as well. If
>>> you're
>>> interested in using it now I would recommend trying the test
>>> version of
>>> VMD (1.8.4a22), which can be dowloaded from
>>> http://www.ks.uiuc.edu/Development/Download/download.cgi.
>>> Alternatively,
>>> I can send you updated files for autopsf alone if you prefer,
>>> although
>>> this option is more complicated.
>>> Peter
>>> rob zehr wrote:
>>>
>>>
>>>
>>>> Hello,
>>>> I am having trouble getting autopsf to work. I would like
>>>> generate a
>>>> psf file from a pdb file of rather simple small molecule. I
>>>> recently
>>>> installed VMD version 1.8.3 with all plugins.
>>>>
>>>> My Problems:
>>>> (1) I cannot find the gui version of autopsf? (..but I can
>>>> load and
>>>> run the TkCon version.)
>>>>
>>>> (2) I get the same error on both my linux and windows machine:
>>>> expected integer but got "none"Not valid molecule id none in
>>>> atomselect's 'molId'
>>>> What does this mean? How do I fix it?
>>>>
>>>> Any help on the matter would be greatly appreciated.
>>>>
>>>> Rob
>>>> ___
>>>> rhzehr_at_hotmail.com
>>>>
>>>>
>>>>
>>
>> --
>> 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
>>
>>
>
> --
> 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
>
> 

--
C. Michael McCallum           http://chemistry.cop.uop.edu/ 
cmccallum.html
Associate Professor
Department of Chemistry, UOP
mmccallum .at. pacific .dot. edu                (209) 946-2636 v  /  
(209) 946-2607 fax