PSF file for a metalloprotein

From: Haleh Abdizadeh (
Date: Mon Dec 09 2013 - 07:29:55 CST

Dear NAMD users,

I am trying to generate a psf file for a metalloprotein in pH of 5.5. I
use psfgen and every thing is fine until I check the pdb file generated by
psfgen and it puts zero coordinates for my metal as if it recognizes the
metal as a part of backbone and since there is no carbon alpha for the
metal, it puts zero coordinates for the backbone. I tried generating psf
file first with Autopsf builder plugged in VMD and then protonating the
residues with shifted pKa but then again psfgen puts zero coordinates for
my metal. Is there any one who could help me with this problem? Thanks a
lot in advance.

Haleh Abdizadeh

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