From: Kwee Hong (joyssstan0202_at_gmail.com)
Date: Mon Aug 09 2010 - 04:29:16 CDT
Hi Bjoern,
Thanks for your reply.
I actually solvate my system with the command below:
package require solvate
solvate 1dmc.psf 1dmc.pdb -t 9 -o 1dmc_wb
And more than 12 water molecules had been added to my system actually.
4 cadmium ions are actually tetrahedrally bound to my protein. So, I've
added the below portion into the parameter file to define the bond between
the sulphur from cystein and the cadmium ion:
SS CD 0.0000 2.4670
The bond lenth was taken from my literature review. I leave the force
constant value at 0.000 as I do not find any such value in my literature
review. I'm afraid that the warning might be referring to this bond length.
If so, what would be its effect to my simulation and does that mean that I
would need to make a guess on that value?
Thanks.
Regards,
Joyce
On Mon, Aug 9, 2010 at 4:13 PM, Bjoern Olausson <namdlist_at_googlemail.com>wrote:
> On Monday 09 August 2010 09:28:16 you wrote:
> > Hi everyone,
> >
> > I'm new to NAMD. While I energy minimized my system, I got a warning as
> > below in the log file:
> >
> > Warning: Ignored 12 bonds with zero force constants.
> >
> > Can anyone tell me what does that mean and how it may affect my
> simulation?
> >
> > Thanks.
> >
> > Regards,
> > Joyce
>
> Hi,
>
> I guess you are using the TIP3 Water model with SHAKE and probably have 12
> Water molecules in your system?
>
> If this is correct, you don't have to worry about the Warning.
>
> Cheers
> Bjoern
>
> --
> Bjoern Olausson
> Martin-Luther-Universität Halle-Wittenberg
> Fachbereich Biochemie/Biotechnologie
> Kurt-Mothes-Str. 3
> 06120 Halle/Saale
>
> Phone: +49-345-55-24942
>
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