Hi all
I have done md simulation with yasara and want to analyze trajectory with gromacs. I used md_convert macro to convert .sim to .xtc format. However gromacs also need .tpr file. How can i get that from yasara?
thanks
Dhiraj
Louis Lategan du Preez
Hi Dhiraj
The tpr file in gromacs is a binary run input file to run a simulation in gromacs - as such it will not be able to generate a useful tpr file from your YASARA output. What you need to do is to save the first frame as a pdb file and then pass the pdb file instead of the tpr file. Make sure that the content of the pdb file is the same as in the xtc file - i.e. that you save the water coordinates in the pdb file as well (else you may get gromacs complaining about atoms that are missing)
Hope this helps
1 votes
1 thanks
- Badges
- Science topic
More Dhiraj Srivastava's questions See All
Similar questions and discussions