From: Peter Freddolino (
Date: Tue Apr 19 2016 - 10:03:52 CDT

For psfgen to work properly, you have to split your molecule into chains and then have a separate segment command for each chain. Note that all of your solvent could be part of one chain if you make the residue numbering unique. You should work through the NAMD tutorial to learn how to do this, and read the psfgen manual. The autopsf package can help to automate the chain splitting process; if you use it, you ought to remove all of the TER cards between urea molecules to avoid generating an excessive number of chains.

> On Apr 18, 2016, at 12:47 AM, Srijita Paul <> wrote:
> this is the pdb file made from packmol and tcl script​ for psfgen i have used.plz forgive me if i have made any silly mistake because i am working on namd only for 4 months.
> <protein_urea.pdb><system.tcl>

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