From: Luis Agullo (LAB) (lab_at_lagullo.com)
Date: Mon Nov 09 2009 - 02:46:52 CST

Thank you for your interest! I generated psf after running this command in
TkCon, but Mg2+ is absent in the output yet. However, something has
changed: Now, VMD recognized the chain O2 in positions 6018 and 6019
(positions of the Mg2+ atoms in pdb) when splitting chains.

Luis

> Luis,
> When he says "sourcing" he means that you should download that script
> to your local computer, put it in a directory where you can get to it
> with VMD, and then run the command "source autopsf.tcl" in the VMD
> text console (or TkCon) before you first open up the AutoPSF window
> in the graphical user interface. If you're not familiar with VMD
> text commands, this might be a good opportunity to briefly try out
> one of the VMD tutorials so you become familiar with how to run scripts
> like this one.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Nov 06, 2009 at 10:58:19AM +0100, Luis Agullo (LAB) wrote:
>> Peter,
>>
>> I do not completely understand what you mean. Could you explain me what
>> I
>> should do step by step? Thank you very much in advance,
>>
>> Luis
>>
>>
>> > Hi Luis,
>> > I found what appears to be the problem -- please try sourcing the
>> > autopsf script at www.ks.uiuc.edu/~petefred/autopsf.tcl prior to
>> opening
>> > the gui, and things should work again.
>> > Thanks for pointing this out.
>> > Best,
>> > Peter
>> >
>> > Luis Agullo (LAB) wrote:
>> >> Of course! I include one of the pdb used attached to this mail.
>> >>
>> >> The process is simple, because I use most of the automatic options
>> found
>> >> in autopsfgen: I open autopsfgen, load the specific stream file for
>> ATP
>> >> in
>> >> addition to the standard topology file, select 'Guess and Split
>> Chains'
>> >> and afterwards I 'Feel Lucky' and obtain the final autopsf file.
>> >>
>> >> Using the same procedure, the previous version maintains Mg2+ in the
>> >> output files.
>> >>
>> >> IMPORTANT NOTES:
>> >> - I use VMD 1.8.7 for Windows!
>> >> - I observed a difference between VMDs when splitting chains
>> (previous
>> >> version of VMD recognize the 2 atoms of Mg2+ in positions 6018 and
>> 6019
>> >> of
>> >> the pdb file; however, the present version found 2 atoms of Mg2+, but
>> at
>> >> positions 6018-12037!?; I attached 2 images to show these different
>> >> results).
>> >>
>> >> Luis
>> >>
>> >>
>> >>
>> >>
>> >>> Hi Luis,
>> >>> could you please send me your input pdb and give me an exact set of
>> >>> steps for reproducing the problem?
>> >>> Thanks,
>> >>> Peter
>> >>>
>> >>> Luis Agullo (LAB) wrote:
>> >>>
>> >>>> Hello,
>> >>>>
>> >>>> I have problems with the last version of VMD (VMD 1.8.7). When
>> using
>> >>>> autopsfgen with a file including Mg2+ (or Ca2+) cation is excluded
>> >>>> from
>> >>>> the output file. This does not take place with the previous of VMD
>> >>>> version
>> >>>> using the same files. I am using the new version for Windows, I
>> have
>> >>>> not
>> >>>> been able to check this in Linux version.
>> >>>>
>> >>>> Cheers,
>> >>>> Luis
>> >>>>
>> >>>>
>> >>>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> ------------------------------------------------------------------------
>> >>>
>> >>>
>> >>> ------------------------------------------------------------------------
>> >>>
>> >
>> >
>> >
>> >
>>
>
> --
> 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
>
>
>