VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Nov 06 2009 - 19:23:54 CST

Hi Luis,
please follow John's instructions -- that is what I meant. Please let me
know if things work properly for you.
Best,
Peter

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