VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Apr 18 2007 - 11:00:26 CDT

As it stands now, you can edit the charges by hand in molefacture, and
make use of paratool
(http://www.ks.uiuc.edu/Research/vmd/plugins/paratool/) to get charges
from QM calculations. I had also been planning to add simpler charge
calculation routines (eg, Gasteiger charges) directly into molefacture,
but haven't yet done so. Obviously, because atomic partial charges are
not uniquely defined, how you get the charges will be determined by what
your intended application is.
Peter

Atila Iamarino wrote:
> 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,
>>> /
>>>
>>>
>>
>>
>>
>
>