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

[ISHRAT JAHAN]

I have selected the whole system while writing the .xtc file and from that
.xtc file i wrote the gro file, then how there is mismatch b/w the
coordinates of  .xtc and .gro file.

On Tue, Aug 22, 2017 at 11:51 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Probably there's a mismatch between the coordinate file you loaded in VMD
> and what's in the XTC. For example, you didn't write the ligand to the XTC.
>
> Mark
>
> On Tue, Aug 22, 2017 at 8:10 AM ISHRAT JAHAN <jishrat17 at gmail.com> wrote:
>
> > ---------- 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.
> > --
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