VMD-L Mailing List

From: Jean-Patrick Francoia (jeanpatrick.francoia_at_gmail.com)
Date: Thu Aug 28 2014 - 15:32:57 CDT

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