# PCA analysis using .DCD

**URL:** <https://gromacs.bioexcel.eu/t/pca-analysis-using-dcd/8209>\
**Category:** User discussions\
**Created:** [February 2, 2024, 2:52pm UTC](https://gromacs.bioexcel.eu/t/pca-analysis-using-dcd/8209 "2024-02-02T14:52:36Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![maham](https://avatars.discourse-cdn.com/v4/letter/m/c77e96/32.png) [@maham](https://gromacs.bioexcel.eu/u/maham)\
**Post date:** [February 2, 2024, 2:52pm UTC](https://gromacs.bioexcel.eu/t/pca-analysis-using-dcd/8209/1 "2024-02-02T14:52:36Z")

</div>

I have simulated my structure using NAMD. later I converted the .dcd file to xtc. i tried to run the gmx covar command but it is giving error to use .tpr file. I have tried to use .gro file but I am still getting the same error.

---

<div class="post-metadata">

**Author:** ![milosz.wieczor](https://avatars.discourse-cdn.com/v4/letter/m/b19c9b/32.png) [@milosz.wieczor](https://gromacs.bioexcel.eu/u/milosz.wieczor)\
**Post date:** [February 2, 2024, 10:10pm UTC](https://gromacs.bioexcel.eu/t/pca-analysis-using-dcd/8209/2 "2024-02-02T22:10:18Z")

</div>

To get a .tpr file for analysis, you might want to convert your topology from NAMD format into Gromacs first (try [ParmEd](https://parmed.github.io/ParmEd/html/index.html)) and use `gmx grompp` with the topology, the .gro, and [a sample mdp file](https://manual.gromacs.org/current/reference-manual/file-formats.html#mdp). Run `gmx grompp -h` for a list of required inputs.