[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.
My system appeared totally broken, unable to understand the error. please
help me to solve this problem.

On Tue, Aug 22, 2017 at 12:10 PM, ISHRAT JAHAN <jishrat17 at gmail.com> wrote:

> 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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