Re: Copper and Zinc: top_all27_prot_lipid.inp

From: Harish Lnu (
Date: Fri Aug 24 2007 - 12:22:11 CDT

Hi Deepangi,
I guess everyone uses same topology file that is meant for proteins/lipids. I never used any special topology file for ZN ions (i have 2-ZN in my protein). There is no special procedure for proteins with metals ( I am sure most of protein assemblies have metals in them as they are the essential coordination content around which a multi-mer is arranged). You definitely are messing up somewhere in making your files from the beginning. Follow the PSFGEN tutorial, make different pdb files for all chains as well as each metal ion (may be you can keep all metal ions in one too--i used different ones to avoid pain of tracing error back), always use tcl commands to write individual pdbs and never do it manually cut/paste way. If you will follow this procedure and track errors it is giving while not recognizing metals, you should be able to write the stuff. You have not mentioned the error it is giving when not recognizing metals, a sample command from my PSFGEN scripts reads metals
as below:
package require psfgen
topology top_phenol.inp

pdbalias residue ZN ZN2
segment X {pdb X.pdb}
coordpdb X.pdb X

pdbalias residue CL CLA
segment Y {pdb Y.pdb}
coordpdb Y.pdb Y

writepdb znj.pdb
writepsf znj.psf

where X.pdb contains all ZN ions separated and Y.pdb has all chloride ions separated.

I hope it helps


Harish Vashisth (Ph.D Candidate)
CAT-361,Chemical & Biological Engg.
Drexel University, Philadelphia, PA
office: 215-895-5823

----- Original Message -----
From: Deepangi Pandit <>
Date: Friday, August 24, 2007 12:51 pm
Subject: namd-l: Copper and Zinc: top_all27_prot_lipid.inp

> Hello:
> 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.
> Question:
> 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.
> Deepangi

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