[gmx-users] converting .gro trajectory to .pdb

[Irem Altan]

Hi,

It gives me an error saying

Fatal error:
Index[1556] 3148 is larger than the number of atoms in the
trajectory file (3145). There is a mismatch in the contents
of your -f, -s and/or -n files.

I’m guessing this is because I had created the original .gro file by just using the protein heavy atoms, but the .tpr file obviously has the indices according to the entire system.

Best,
Irem

On Jan 18, 2017, at 4:22 PM, Dawid das <addiw7 at googlemail.com<mailto:addiw7 at googlemail.com>> wrote:

Hi,

I guess you can try
gmx trjconv -f  file.gro -o file.pdb -pbc mol -s file.tpr -center

2017-01-18 16:14 GMT+01:00 Irem Altan <irem.altan at duke.edu<mailto:irem.altan at duke.edu>>:

Hi,

I have a trajectory saved in .gro format. It has multiple frames/snapshots
in it. I’m using .gro format because I needed higher precision than
standard .pdb precision, but now I can’t visualize it with VMD. I would
like to convert this to .pdb, and I tried editconf to do this. The problem
is, it only converts the first frame. How can I convert the entire
trajectory from .gro to .pdb?

Best,
Irem
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