VMD-L Mailing List

From: Jean-Patrick Francoia (jeanpatrick.francoia_at_gmail.com)
Date: Thu Aug 28 2014 - 16:13:29 CDT

Ok. Actually, exporting the minimized structure to mol2 file with
Spartan created the issue.

If I open the file with Avogadro, the program automatically assigns the
charges. Then I just need to save it with this program again.

Solved the issue.

Thanks

Le 28/08/2014 22:40, John Stone a écrit :
> Sounds like the mol2 file doesn't get you charge information, so you're
> either going to load a file that does contain charges, set the per-atom
> partial charges yourself via scripting, or else use an external utility
> or script to assign them if you don't have them assigned otherwise.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Thu, Aug 28, 2014 at 10:32:57PM +0200, Jean-Patrick Francoia wrote:
>> It says 179 atoms. And there are 179 atoms in the molecule.
>> I would normaly expect 9.
>>
>> So that is the issue. How can I assign charges to the (good) atoms ?
>>
>> Le 28/08/2014 22:31, John Stone a écrit :
>>> The warning comes from some parts of your structure not having
>>> charges assigned in the input files that VMD (and later APBS) are
>>> being provided. One way to check how many atoms lack charge in VMD
>>> is do to something like this:
>>> set sel [atomselect top "charge == 0"]
>>> $sel num
>>>
>>> That will tell you how many atoms are uncharged...
>>>
>>> Cheers,
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>>
>>> On Thu, Aug 28, 2014 at 10:00:58PM +0200, Jean-Patrick Francoia wrote:
>>>> Hello,
>>>>
>>>> I have created an octapeptide of lysine (see mol2 file attached:
>>>> https://www.dropbox.com/s/nl6lq9ow5exo8dw/G1_min.mol2?dl=0) with a
>>>> certain manner.
>>>> I then "minimized" the structure with Spartan. That's a rough (and
>>>> probably wrong) minimization, but I just need an idea of the 3D
>>>> structure of my molecule. (Please do not focus on this part, this
>>>> molecule is only an example, and the way I build it cannot be changed).
>>>>
>>>> Finally, I would like to create an electrostatic potential map for this
>>>> molecule. The matter is APBS tells me my molecule is not charged. I
>>>> would like to understand why it keeps telling me that.
>>>> I have some -NH3+ functions on my molecule (8 to be correct), and one
>>>> carboxylic acid deprotonated. So the charge should be 7.
>>>>
>>>> Maybe it is because the structure is correct, but the charge of each
>>>> atom is not reported in a mol2 file ?
>>>>
>>>> I would like to understand what the problem is, and find a way to
>>>> correct it. Could you give me a hand ?
>>>>
>>>> Sincerely