[gmx-users] Can't load converted trajectory on to vmd

[Mark Abraham]

Hi,

As the VMD documentation probably says somewhere, you can't load a
trajectory into a molecule with a different number of atoms. So make a gro
file that matches the atom number and ordering of your trajectory, e.g with
trjconv.

Mark

On Tue, 12 May 2015 10:32 Seera Suryanarayana <palusoori at gmail.com> wrote:

> Dear gromacs users
> I have executed the trjconv command for generating the .xtc file to futher
> analysis.  I have selected protein for output. I loaded the .gro file on to
> vmd  and then I tried to load .xtc file on to vmd. But, I couldn't load it
> and I got the following error.
>
> vmd > Info) Using plugin gro for structure file
> /Extended/Dynamics/Hub_simulation/Gpu_md/1ycs/500ns/tmp/md_0_1.gro
> Info) Using plugin gro for coordinates from file
> /Extended/Dynamics/Hub_simulation/Gpu_md/1ycs/500ns/tmp/md_0_1.gro
> Info) Determining bond structure from distance search ...
> Info) Analyzing structure ...
> Info)    Atoms: 35183
> Info)    Bonds: 24477
> Info)    Angles: 0  Dihedrals: 0  Impropers: 0  Cross-terms: 0
> Info)    Bondtypes: 0  Angletypes: 0  Dihedraltypes: 0  Impropertypes: 0
> Info)    Residues: 10932
> Info)    Waters: 10738
> Info)    Segments: 1
> Info)    Fragments: 10742   Protein: 1   Nucleic: 0
> Info) Finished with coordinate file
> /Extended/Dynamics/Hub_simulation/Gpu_md/1ycs/500ns/tmp/md_0_1.gro.
> ERROR) BaseMolecule: attempt to init atoms while structure building in
> progress!
> ERROR) Invalid number of atoms in file: 2966
> Info) Using plugin xtc for coordinates from file
> /Extended/Dynamics/Hub_simulation/Gpu_md/1ycs/500ns/tmp/md_0_1_noPBC.xtc
> ERROR) Incorrect number of atoms (2966) in
> ERROR) coordinate file
> /Extended/Dynamics/Hub_simulation/Gpu_md/1ycs/500ns/tmp/md_0_1_noPBC.xtc
> Info) Finished with coordinate file
> /Extended/Dynamics/Hub_simulation/Gpu_md/1ycs/500ns/tmp/md_0_1_noPBC.xtc.
>
> Based on above information what I understood is that the .gro file has
> 35183 atoms including solvent atoms. But in .xtc file has only protein
> atoms as I have selected protein as output during trjconv execution.
> Actually I want to load only protein molecule on to vmd after mdrun. Kindly
> tell me how to overcome this problem.
>
> Thanks in Advance
> Surya
> Graduate student
> India.
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