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 - 04:00:03 PDT
