From: Syed Kashif Zafar (skashifzafar_at_yahoo.com)
Date: Sun Apr 15 2012 - 23:28:49 CDT
No worry from warning. in the case of simulation unstable many others case are also involved. just try to run it after increasing the cut off value
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From: Vidhya Sankar <vidhyasankar7928_at_yahoo.com>
To: Syed Kashif Zafar <skashifzafar_at_yahoo.com>; "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
Sent: Saturday, April 14, 2012 11:27 PM
Subject: psfgen warnings
Dear Namd user
i have created the psfgen using Autopsfbuilder while i create i got warnings like this
Info: guessing coordinates for 8784 atoms (8 non-hydrogen)
Warning: poorly guessed coordinates for 71 atoms (8 non-hydrogen):
Warning: poorly guessed coordinate for atom HT1 VAL:1 P1
Warning: poorly guessed coordinate for atom HT2 VAL:1 P1
Warning: poorly guessed coordinate for atom HT3 VAL:1 P1
Warning: poorly guessed coordinate for atom HG2 PRO:4 P1
Warning: poorly guessed coordinate for atom HG2 PRO:37 P1
Warning: poorly guessed coordinate for atom HG2 PRO:77 P1
Warning: poorly guessed coordinate for atom HG2 PRO:95 P1I ignore the warnings and run the simulation i got Constraint failure in RATTLE algorithm for atom 13596! and simulation become unstable
please assist me in avoiding the Warning I am using Different topology file to construct psfgen files Every time shows same error (Warning: poorly guessed coordinate for atom HT1 VAL:1 P1)
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