Hello Urszula
I have tried to do by cada. But, I could not copy
"leaprc.zinc", "znb.lib", "hydroxide.lib" , "hin.lib" and
"frcmod.zinc" to the cmd, lib and parm folder. So, I have kept them in
that folder from where I am doing everything. I have changed HYS to
HIN , one GLU to GLH and the residue name of zinc to ZNB. When I give
the command "source leaprc.zinc" in xleap, some error massages are
coming. I load each library file in xleap. Then as soon as I load my
pdb file "2CBA.pdb" in xleap, xleap is vanishing. And, some error
message are coming in terminal. I have removed the last lines of pdb
file. So, what can I do?
sanjib
On 5/23/12, Urszula Uciechowska <urszula.uciechowska.chem.umu.se> wrote:
>
> you may try to use this apporach:
> http://mayoresearch.mayo.edu/mayo/research/camdl/zinc_protein.cfm
>
> /Urszula
>
> ________________________________________
> Von: Sanjib Paul [sanjib88paul.gmail.com]
> Gesendet: Mittwoch, 23. Mai 2012 10:50
> An: amber.ambermd.org
> Betreff: [AMBER] how to introduce Zn2+ in amber
>
> Hii..
> I want to set up HCA II in amber. But i can't introduce Zn2+ to
> amber. I have followed TUTORIAL A1 old "buliding your own custom
> residue". I have created a pdb file of zinc, tried to add atom type in
> unit editor. But, I can't do it. Actually, I can't select any menu in
> unit editor.
> What is actually happening? Please inform me.
>
> sanjib
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Received on Wed May 23 2012 - 22:00:03 PDT
