VMD-L Mailing List

From: Jean-Patrick Francoia (jeanpatrick.francoia_at_gmail.com)
Date: Thu Aug 28 2014 - 15:00:58 CDT

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