[gmx-users] cannot load the xtc file (without PBC) to VMD

[Justin Lemkul]

On 1/13/20 5:35 AM, Lalehan Ozalp wrote:
> Dear all, I have a question regarding loading .xtc file (with no periodic
> boundary conditions) to VMD which I generated before. To this end, I had
> used the command:
> trjconv -f md_0_10.xtc -s md_30.tpr -n index.ndx -o noPBC.xtc -pbc mol -ur
> compact -center
> and selected *protein* for centering, and *system* for output.
> However, when I load my corresponding gro file to VMD, and then loading the
> xtc file above, the following error occurs:
>
> ERROR) BaseMolecule: attempt to init atoms while structure building in
> progress!
> ERROR) Invalid number of atoms in file: 132259
> Info) Using plugin xtc for coordinates from file
> /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc
> ERROR) Incorrect number of atoms (132259) in
> ERROR) coordinate file /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc
> ERROR) Mismatch between existing molecule or structure file atom count and
> coordinate or trajectory file atom count.
> Info) Finished with coordinate file
> /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc.

The error implies you've loaded a mismatched coordinate file for this 
trajectory, or otherwise didn't save the number of coordinates you 
thought you did with trjconv. This is really more of a VMD problem, so 
you may find better support on their mailing list.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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