From: Radak, Brian K (bradak_at_anl.gov)
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.
Leadership Computing Facility
Argonne National Laboratory
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From: Sarath Josh M.K [sarathjoshmk_at_gmail.com]
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: sarathjoshmk_at_iiserkol.ac.in<http://iiserkol.ac.in>; Mobile: +91-9447184430
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