RE: PSFgen failed to guess coordinate due to bad angle CD CG HG2

From: Radak, Brian K (
Date: Fri Feb 10 2017 - 09:36:22 CST

When generating new atoms, coordinates will only be guessed if you use the "guesscoord" command - this will only work if you have enough coordinates at that time to establish a coordinate frame (usually at least 3 atoms).

Can you post your script?

P.S. It is always best to reply to the NAMD list so that other experienced users have a chance to respond and so the responses are stored in the list archive for users who have a similar problem in the future.

Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory

9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
From: Sarath Josh M.K []
Sent: Friday, February 10, 2017 5:09 AM
To: Radak, Brian K
Subject: namd-l: PSFgen failed to guess coordinate due to bad angle CD CG HG2

Dear Dr. Brian Radak,
Thanks for your expert openion. I tried to build with coord command and the psf and pdb generated. The pdb generated added hydrogen atoms but the coordinates are missing.!! Can you please comment on this problem.


        Sarath Josh M.K.

        SERB- National Post Doctoral Fellow

        Department of Biological Sciences

        Indian Institute of Science Education and Research, Kolkata

        Nadia District, Mohanpur-741246

        West Bengal, India

        E-mail:<>; Mobile: +91-9447184430


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