VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Aug 13 2012 - 02:34:56 CDT

Hi all:
I used often the latest VMD on Linux to evaluate correctly the charge
on a system as indicated by the output below. In contrast, for systems
having lysine protonated at the side chain (-NH3), I am getting charge
zero, while there is no neutralizing negative charge on the system.
Thus I tried with the minimal system of lysine capped with ACE and
NME:

Main console display active (Tcl8.5.6 / Tk8.5.6)
(ACE_LYS_NME) 1 % set everyone [atomselect top all]
atomselect0
>Main< (ACE_LYS_NME) 2 % puts "TOTAL CHARGE ON THE SYSTEM: [eval vecadd [$everyone get charge]]"
TOTAL CHARGE ON THE SYSTEM: 0.0
>Main< (ACE_LYS_NME) 3 %

When the above system is subjected to ab initio calculation - by any
code - the charge has to be set to +1.

Thanks for advice

francesco pietra