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From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Fri Jul 24 2015 - 18:00:32 CDT
You would be much better off using AutoPSF for a task like this. PSFgen alone will treat your protein like a single connected chain (so residues either side of a gap will become connected to each other) and, as you have already discovered, won't automatically handle ligands. AutoPSF is the front-end that handles all of that before feeding to PSFgen, and can be called from a non-interactive script.
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Thank you very much for your suggestions.
As you said, i have started with the tcl script (shown below), i am able to upload all the molecules in one go, but for some reason the output psf and pdb do not show any atoms. can anyone please help me to correct the script--_000_EF433A3AECDD45F9A0BE1A2783576F4Aquteduau_--