Re: System net charge

From: Cruz-Chu Eduardo Roberto (eduardo.cruz_at_inf.ethz.ch)
Date: Thu Aug 04 2011 - 03:28:45 CDT

well, all that charge must come from somewhere. Check the charge of your lipids by doing:

set selLipid [ atomselect top lipid ];
measure sumweights $selLipid weight charge;

the same for the other parts of your system: water, ions, proteins, and whatever else you have there, until you find the charged part. I would guess that the lipids are not properly protonated.

On Aug 3, 2011, at 2:20 AM, Andres Morales N wrote:

Hi Eduardo!

DPPC molecule is zwitteronic having a negative charge on the phosphate group and a positive charge on the amine. So I would not nedd to add any ions but I get the same mistake:

Autoionize) System net charge after adding ions: -2584.480033516884e
> WARNING: System has a non-integer total charge. There was likely a problem in the process of building it.

Thanks for your help

 Hernán Andrés Morales Navarrete

Biophysics and Molecular Modeling Group
Physics Department
Escuela Politécnica Nacional, Quito - Ecuador
Ladrón de Guevara E11-253.
Casilla 17-01-1253
http://www.ciencias.epn.edu.ec/~biomod/

> From: eduardo.cruz_at_inf.ethz.ch<mailto:eduardo.cruz_at_inf.ethz.ch>
> To: andresmoralesn2_at_hotmail.com<mailto:andresmoralesn2_at_hotmail.com>
> Subject: Re: namd-l: System net charge
> Date: Fri, 29 Jul 2011 08:46:16 +0000
>
> Hi Andres;
>
> No, it is not correct. What is the charge of a single DPPC molecule?. If DPPC is charged, you will need as many counterions as lipid charges to get zero.
>
> Regards;
>
> Eduardo
>
>
>
> On Jul 29, 2011, at 10:25 AM, Andres Morales N wrote:
>
> Dear NAMD Users:
>
> I built a system with a dppc lipid bilayer plus water. But I got the following mistake:
>
>
> Autoionize) System net charge after adding ions: -2584.480033516884e
> WARNING: System has a non-integer total charge. There was likely a problem in the process of building it.
>
>
> Is it correct that the system has this amount of charge?
>
> The script I used was:
>
> ########################################################################
> mol new dppc.psf
> mol addfile dppc.pdb
>
> package require solvate
> solvate dppc.psf dppc_tem.pdb -z 5 +z 50 -o dppc_water
>
>
> set sel [atomselect top all]
> set netCharge0 [eval "vecadd [$sel get charge]"]
> $sel delete
>
> ### Neutralizar el sistema: añadimos 8 iones Cl y 4 iones Na. Y calcular la carga neta del Nuevo sistema
> resetpsf
> package require psfgen
> package require autoionize
>
> autoionize -psf dppc_water.psf -pdb dppc_water.pdb -nna 4 -ncl 8
>
> ###########################################################################
>
> I also used the dppc files (pdb and psf) from membrane tutorial files of NAMD. (http://www.ks.uiuc.edu/Training/Tutorials/science/membrane/)
>
>
> Thanks for your help
>
>
> Hernán Andrés Morales Navarrete
>
> Biophysics and Molecular Modeling Group
> Physics Department
> Escuela Politécnica Nacional, Quito - Ecuador
> Ladrón de Guevara E11-253.
> Casilla 17-01-1253
> http://www.ciencias.epn.edu.ec/~biomod/
>
>
>
>

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