Copper and Zinc: top_all27_prot_lipid.inp

From: Deepangi Pandit (
Date: Fri Aug 24 2007 - 11:51:39 CDT

        I am new to molecular dynamics simulations. I am trying to
learn NAMD with the help of tutorials. When I try to generate Protein
Structure File (psf) for my protein using topology file
top_all27_prot_lipid.inp, the program is unable to recognize Zinc and
Copper in the protein. I checked the .inp listed above. I was able to
find ZN but no CU. I am not sure why program was unable to recognize
ZN when it is listed in the .inp file.


1 Which topology file should be used if I have metals in my protein?
If there is no

2. Are there any special procedures to be followed for proteins with metals?

I am not sure if question is trivial but I was unable to find the
solution even after going through the namd list.

Thank you.

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