I am working with a protein-peptide complex. I aim to do mutations on the peptide. I was performing mutation free energy calculations using the Fast growth method following the tutorial of the Trp cage. When I use pmx analyse to do the Free Energy estimation it gives me an error which says “no good dgdl files were provided”. Suspecting something wrong my files, I tried the calculation with the files from the tutorial and the problem still persists. Has anyone ever faced this problem? And how do I solve it? Any help would be much appreciated.
A screenshot of the error is attached.
Hi,
If you are using pmx develop branch (installation: pmx/tutorials/INSTALL at develop · deGrootLab/pmx · GitHub) for the tutorial (Mutation free energy calculations), then either " pmx analyse -fA eqA/morphes/frame*/dgdl.xvg -fB eqB/morphes/frame*/dgdl.xvg -t 300 --nbins 25" or “./analyze_dhdl.py -fA eqA/morphes/frame*/dgdl.xvg -fB eqB/morphes/frame*/dgdl.xvg -t 300 --nbins 25” should work fine (both of them work fine for me).
Could you please post the command you used, if the problem still persists?
All the best.
Hi,
Thank you for your reply. There was something wrong with my previous installation. I installed pmx again and it worked fine. And for reference I used
pmx analyse -fA path_to_forward/frame*/dgdl.xvg -fB path_to_backward/frame*/dgdl.xvg -t 300 --nbins 25
Best,
Shounak