Dear Sanjib,
Read about the CaDA approach (e.g. from the page you got the files from and
references mentioned there) and you'll see that the whole point of the
approach is to have dummy atoms around the zinc (more or less representing
d-orbitals).
You certainly DON'T want to remove the dummy atoms.
--Marc
On 25 May 2012 11:30, Sanjib Paul <sanjib88paul.gmail.com> wrote:
> Dear amber user and developer,
> I used CaDA to identify Zn2+ in human carbonic
> anhydrase II. So, I used the files given in the web page of CaDA. The
> files are leaprc.zinc, hydroxide.lib, znb.lib, hin.lib, frcmod.zinc. I
> followed everything instructed on that page. When I upload leaprc.zinc
> file in xleap, some error messages are coming. Neglecting that, I
> upload every library and frcmod file in xleap. Then solvating the
> system, I generate prmtop file and inpcrd file. Then I create a pdb
> file from prmtop and inpcrd file. And, on uploading the pdb file on
> VMD I see there is four dummy atom around zinc bonded with it. So, I
> think, it is no more actual protein structure. So, what should I do
> now? How can I remove these dummy atoms?
> Sanjib
>
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Received on Fri May 25 2012 - 04:00:04 PDT
