From: Stefan Doerr (
Date: Thu Jul 07 2016 - 05:22:17 CDT

As for automatic, I don't really think so. Because building with psfgen
doesn't just rename atoms, it also adds missing atoms. So the order of
atoms will be changed and you cannot do a 1-1 mapping between atoms in the
original PDB and the built PDB. You probably could do automatic residue
name mapping though since psfgen should not be adding any new residues.

On Thu, Jul 7, 2016 at 12:19 PM, Stefan Doerr <> wrote:

> Coor files only contain coordinates, no atom names or residue names. So
> yeah if you modify the psf or pdb manually to put back the original residue
> names it should load fine.
> On Thu, Jul 7, 2016 at 11:51 AM, Kevin C Chan <
> > wrote:
>> Dear Users,
>> Psfgen as a default would alias some atom names in order to run NAMD
>> afterwards. I am wondering, instead of running psfgen again with inverted
>> alias, is there a convenient way of changing the names of a pdb after MD
>> simulations (written from a coor file) back to what we see in a pdb from
>> the RCSB PDB bank?
>> Any experience shared would be appreciated.
>> Thanks,
>> Kevin
>> City University of Hong Kong