Re: getting desired angle

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>
>> wrote:
>> > 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.

axel.

-- 
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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