Hi all,
I tried following what was in the tutorial on how to run production MD using pmemd.cuda. It worked perfectly fine when I did the heating step, but when I tried running for production it says:
production.sh: line 5: home/itsrdc/amber20/bin/pmemd.cuda: No such file or directory
I tried doing it manually (outside the bash file) by inputting the following:
(base) itsrdc.itsrdc:~/Desktop/Amber_5O5T$ export CUDA_VISIBLE_DEVICES=0
(base) itsrdc.itsrdc:~/Desktop/Amber_5O5T$ $AMBERHOME/bin/pmemd.cuda -O -i prod1mpi.in -o psma_prod.out -p psma_pmemdcuda.parm7 -c psma_heat.nc -ref psma_pmemdcuda.rst7 -x psma_prod.nc -inf psma_prod.mdinfo
Then this appeared:
STOP PMEMD Terminated Abnormally!
I am not sure where did I go wrong. I tried checking the generated output file of the production MD and it just says:
ERROR: NetCDF restart has Conventions that are not AMBERRESTART.
| ERROR: Could not read second line of psma_heat.nc
Bad inpcrd file!
I tried running sander just to try my luck but this time this line already appeared:
ERROR: I could not find the number of atoms or the time on the second line of your inpcrd file [psma_heat.ncrst]
How can I recompile pmemd.cuda only? Or do I have to recompile? Thank you for your help.
Joanna Michelle Chua-Aniago, RPh
Science Research Specialist II
Isotope Techniques Section
Nuclear Services Division
Philippine Nuclear Research Institute
Tel. no. (+632) 8929 6011 to 14 loc. 240
Mobile No. (+63) 917 845 4137
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Received on Mon Mar 20 2023 - 16:00:02 PDT
