From: hannes.loeffler_at_stfc.ac.uk
Date: Mon Apr 16 2012 - 02:35:35 CDT
A few poorly guessed hydrogen coordinates should really not be a problem. Have you done any energy minimisation before having embarked upon the MD run? Also note that the constraint failure occured in atom 13596 (your initial structure has only 8784 atoms). Have you checked if that atom is anywhere close to the poorly guessed hydrogens?
Hannes.
________________________________________
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of Vidhya Sankar [vidhyasankar7928_at_yahoo.com]
Sent: 15 April 2012 07:27
To: Syed Kashif Zafar; namd-l_at_ks.uiuc.edu
Subject: namd-l: 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 P1
I 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)
-- Scanned by iCritical.
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