From: Andres Morales N (andresmoralesn2_at_hotmail.com)
Date: Thu Aug 04 2011 - 23:43:11 CDT
Hi Eduardo
Thanks for your help. The problem was that the lipids are not properly protonated.
> To: andresmoralesn2_at_hotmail.com
> CC: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: System net charge
> Date: Thu, 4 Aug 2011 08:28:45 +0000
>
> 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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