From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Oct 25 2010 - 08:08:30 CDT
On Sun, Oct 24, 2010 at 11:06 PM, Kwee Hong <joyssstan0202_at_gmail.com> wrote:
> On Mon, Oct 25, 2010 at 7:06 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>> On Sat, Oct 23, 2010 at 4:49 AM, Kwee Hong <joyssstan0202_at_gmail.com>
>> > Hi.
>> > My protein is bound to one cadmium ion.
>> > I've inserted the relevant parameter value which I got from the
>> > literature
>> > into the force field file.
>> did you also define the corresponding interactions, e.g. bonds,
>> angles, dihedrals and so on in the .psf file?
> They are all auto-defined in the .psf file.
are you certain? have you check them?
since you have some unusual structure, i would not
trust any automatic tool to generate those, particularly
if the results don't match your expectations.
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://sites.google.com/site/akohlmey/ Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
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