From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Aug 13 2012 - 05:13:41 CDT

On Mon, Aug 13, 2012 at 11:45 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Mon, Aug 13, 2012 at 11:38 AM, Francesco Pietra
> <chiendarret_at_gmail.com> wrote:
>> List added, sorry for previous mail
>
> please make it a habit. it is very annoying
> to have to remind people all the time.
>
>>> Axel: I don't understand what you mean. I am not dealing with MD,
>>> rather with ab initio, and DFT, calculations. Just drawn a system - as
>>> above - collected the Cartesian coordinates, and subjected to the ab
>>> initio, or DFT, code. Correctly when the charge is set to +1. I
>>> thought that VMD, with the above script, reports the charge correctly.
>>> I must be misusing VMD, or I am completely out the way.
>
> so if you are not feeding VMD any information, where should it come from?
> you don't say in what format you read in data before you run your script.
>
> VMD is a *visualization* and *analysis* tool. it has absolutely no knowledge
> of chemistry, only a little bit of protein oriented heuristics here and there.
>
> in other words. the total charge will *always* be zero unless you set the
> individual charges of the atoms some something, eg. through loading a
> suitably generated file, which contains the respective charge information.
>
> that is what i meant with GI-GO,

I took the lesson with thanks
francesco

PS: when I was successful, I used a sybyl mol2 file, not a pdb like now.

> axel.
>
>>>
>>> thanks
>>> francesco
>>>
>>>
>>>>
>>>> GI-GO
>>>>
>>>> axel
>>>>
>>>>
>>>>>
>>>>> francesco pietra
>>>>
>>>>
>>>>
>>>> --
>>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>>>> International Centre for Theoretical Physics, Trieste. Italy.
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.