RE: dcd to pdb conversion

From: Radak, Brian K (
Date: Wed Jan 04 2017 - 10:43:35 CST

As indicated by others, you can't really do what you describe with NAMD - that task is much better accomplished with VMD (for which there is a separate listserv that I would recommend directing your question to).

Am I correct in suspecting that you just want to probe interaction energies or order parameters between pairs of fragments? This can be accomplished with NAMD and almost certainly does not require generation of additional PDB files.


Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory

9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
From: [] on behalf of Srijita Paul []
Sent: Wednesday, January 04, 2017 6:18 AM
To: NAMD list
Subject: namd-l: dcd to pdb conversion

I am using a system which contains 4 different types of molecule.Now I want to extract coordinates of any two kind of molecules among the 4 molecules from the dcd file to a pdb file.I have one tcl script to convert dcd to pdb which is attached here but it is working only for one molecule or for all molecules.Is there any way to select two different moleule or resname in the script?

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