VMD-L Mailing List

From: Luis Agullo (LAB) (lab_at_lagullo.com)
Date: Fri Nov 06 2009 - 03:58:19 CST

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
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>
>
>
>