Errors on Missing Atoms for Some Bonds

From: Taekyung Kwon (scienbox_at_gmail.com)
Date: Sun Nov 30 2008 - 22:19:29 CST

Hello NAMD users,

I have a problem in making psf file with psfgen.

Error massage is ..
------
Info: generating structure...
ERROR: Missing atoms for bond N(0) C12(0) in residue CDMP:1
ERROR: Missing atoms for bond N(0) HN(0) in residue CDMP:1
ERROR: Missing atoms for bond C(0) N(0) in residue CDMP:1
ERROR: Missing atoms for bond C(0) O(0) in residue CDMP:1
ERROR: Missing atoms for bond C(0) C41(0) in residue CDMP:1
..
Warning: failed to set coordinate for atom C CDMP:1 O1
Warning: failed to set coordinate for atom O CDMP:1 O1
Warning: failed to set coordinate for atom N CDMP:1 O1
Warning: failed to set coordinate for atom HN CDMP:1 O1
------

Then, PSFGEN made a psf file not containing 4 atoms and split it into
2 fragments.
I could see 4 atoms and 5 bond definitions in the topology file are
correct.

Do you have any idea on this? If yes, could you tell me the idea?
Thank you!

Best,

Taekyung.
---------------------------------------------
Taekyung Kwon
Visiting Scientist
Department of Neuroscience
Albert Einstein College of Medicine
Yeshiva University
Bronx, NY, USA

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