VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Nov 05 2009 - 20:02:41 CST

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
>>>
>>>
>>>
>>
>>
>>
>>
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