[gmx-users] Fwd: Unusual bonding between residues in vmd

[ISHRAT JAHAN]

---------- Forwarded message ----------
From: ISHRAT JAHAN <jishrat17 at gmail.com>
Date: Tue, Aug 22, 2017 at 11:35 AM
Subject: Unusual bonding between residues in vmd
To: gromacs.org_gmx-users at maillist.sys.kth.se


Dear all,
I was trying to do the simulation of 100 ns of protein and drug in gromacs
v- 5.1.4 using amber99sb.ff but i have stopped the simulation in between
i.e at 40 ns. By using 40 ns .xtc file i have generated .gro file after
applying pbc condition and when i load the .gro file in  Vmd i got the
followung error-
Warning) Unusual bond between residues:  509 (none) and 20136 (waters)
Warning) Unusual bond between residues:  509 (none) and 25255 (waters)
Warning) Unusual bond between residues:  509 (none) and 25255 (waters)
Warning) Unusual bond between residues:  509 (none) and 19182 (waters)
Warning) Unusual bond between residues:  509 (none) and 19206 (waters)
Warning) Unusual bond between residues:  510 (none) and 12546 (waters)
Warning) Unusual bond between residues:  510 (none) and 18490 (waters)
Warning) Unusual bond between residues:  510 (none) and 18490 (waters)
Warning) Unusual bond between residues:  510 (none) and 18557 (waters)
Warning) Unusual bond between residues:  510 (none) and 18599 (waters)
Warning) Unusual bond between residues:  510 (none) and 19269 (waters)
Warning) Unusual bond between residues:  510 (none) and 19281 (waters)
Warning) Unusual bond between residues:  510 (none) and 19667 (waters)
Warning) Unusual bond between residues:  510 (none) and 19667 (waters)
Warning) Unusual bond between residues:  510 (none) and 24324 (waters)
Warning) Unusual bond between residues:  510 (none) and 25047 (waters)
Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
Warning) Unusual bond between residues:  510 (none) and 18599 (waters)
Warning) Unusual bond between residues:  510 (none) and 19248 (waters)
Warning) Unusual bond between residues:  510 (none) and 19248 (waters)
Warning) Unusual bond between residues:  510 (none) and 20005 (waters)
Warning) Unusual bond between residues:  510 (none) and 20005 (waters)
Warning) Unusual bond between residues:  510 (none) and 24324 (waters)
Warning) Unusual bond between residues:  510 (none) and 12450 (waters)
Warning) Unusual bond between residues:  510 (none) and 12450 (waters)
Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
Warning) Unusual bond between residues:  510 (none) and 12928 (waters)
Warning) Unusual bond between residues:  510 (none) and 18599 (waters)
Warning) Unusual bond between residues:  510 (none) and 18599 (waters)
Warning) Unusual bond between residues:  510 (none) and 24324 (waters)
Warning) Unusual bond between residues:  510 (none) and 24324 (waters)
Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
Warning) Unusual bond between residues:  510 (none) and 18599 (waters)
Warning) Unusual bond between residues:  510 (none) and 19248 (waters)
Warning) Unusual bond between residues:  510 (none) and 24324 (waters)

Will anyone help me to solve the above problem.
Thanks in advance.