From: Axel Kohlmeyer (
Date: Mon Aug 13 2012 - 03:37:08 CDT


On Mon, Aug 13, 2012 at 9:34 AM, Francesco Pietra <> wrote:
> 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]]"
>>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

with classical MD, you get out what you put in.
if your system has not the correct charge, then
your topology/parameter file is incorrect.
VMD can only use the information that you provide.



> francesco pietra

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.