Re: PSF file for a metalloprotein

From: Roy Fernando (
Date: Mon Dec 09 2013 - 09:57:32 CST

Hi Haleh,

I did something similar sometime ago.

According to how I understand the process, to construct the psf file you
need to have the details of the bonds written in the topology file. Usually
the standard topology files do not carry information regarding specific
metal sites. So you will have to edit the topology file manually. I think
you will have to apply a patch containing the metal site after creating the
backbone segments.

You will find useful information in the topology file section in the
appendix of the NAMD tutorial and in Topology file tutorial.

I also think you can use topotools plugin to do the changes to the existing
psf structure and save a new pasf file.


On Mon, Dec 9, 2013 at 8:29 AM, Haleh Abdizadeh

> 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.
> Best,
> Haleh Abdizadeh

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