VMD-L Mailing List

From: Atila Iamarino (atila_at_usp.br)
Date: Wed Apr 18 2007 - 10:50:57 CDT

I reinstalled vmd 1.8.6 and it worked just fine. Does molefacture or any
other plugin calculate the charges of the molecule that I created?

My best,

Peter Freddolino wrote:
> Please let me know if it still doesn't work after you reinstall.
> Peter
>
> Atila Iamarino wrote:
>
>> Peter Freddolino wrote:
>>
>>> Sorry, it should be
>>> $sel writemol2
>>> not
>>> $sel write mol2
>>>
>>> You can also access this through the File->Save coordinates menu in the
>>> vmd gui.
>>> Peter
>>>
>>> Atila Iamarino wrote:
>>>
>>>
>>>> Peter Freddolino wrote:
>>>>
>>>>
>>>>> Hi Atila,
>>>>> for now, you can read the xbgf file in the normal vmd interface, and
>>>>> then save a mol2 file using $sel writemol2 or the graphical interface.
>>>>> If people would like to write mol2s straight from molefacture, this is
>>>>> trivial to add to future versions.
>>>>> Please let me know if this doesn't make sense.
>>>>> Best,
>>>>> Peter
>>>>>
>>>>>
>>>>> Atila Iamarino wrote:
>>>>>
>>>>>
>>>>>
>>>>>> Hi,
>>>>>> I'm starting to use VMD and I have used the molefacture to make bonds
>>>>>> and place hydrogens in my molecule. Now I want to save the xbgf file
>>>>>> in mol2 butt I don't know how.
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>> It makes sense yes. I did'nt know the comand write after selection.
>>>> Anyway when I use
>>>> $sel1 write mol2
>>>> it says that this file type is unknown
>>>>
>>>>
>>>>
>>>
>>>
>> I found what happens. VMD gives the error /Rejecting plugin with
>> incorrect ABI version:
>> i'm going to reinstall the program and see what happens.
>> Thank you very much,
>> /
>>
>>
>
>
> 

-- 
Atila Iamarino
L.E.M.B. - Laboratory of Molecular Evolution and Bioinformatics
Av. Prof. Lineu Prestes, 1734 - USP (University of São Paulo) - ICB
Zip: 05508-000 Phone: +55 11 30917290 / +55 11 30918453