it looks like there are different things going wrong in different spots.
for the error about the netcdf restart, you might be trying to load a
trajectory (psma_heat.nc) as the input coordinates (the -c flag). if this
is indeed a trajectory (saved with the -x flag), then use the restart file
form that run instead. since you didn't provide the full script we can't
see what that was called. in the sample, though, I don't see you saving a
restart (-r flag), so you'll need to look at your output and see if you
saved one from the prior run, and adjust this script to include one.
for the first error (pmemd.cuda not found), try typing "ls $AMBERHOME/bin".
again since we don't see the production.sh file it's hard to know if
AMBERHOME was set there or not. the error says " production.sh: line 5:
home/itsrdc/amber20/bin/pmemd.cuda: No such file or directory", but I
suspect that there should be a "/" before home.
if these don't work, try sharing your full production.sh file.
On Mon, Mar 20, 2023 at 6:48 PM Joanna Michelle E. Chua via AMBER <
amber.ambermd.org> wrote:
> Hi all,
>
> I tried following what was in the tutorial on how to run production MD
> using pmemd.cuda. It worked perfectly fine when I did the heating step, but
> when I tried running for production it says:
>
> production.sh: line 5: home/itsrdc/amber20/bin/pmemd.cuda: No such file or
> directory
>
> I tried doing it manually (outside the bash file) by inputting the
> following:
>
> (base) itsrdc.itsrdc:~/Desktop/Amber_5O5T$ 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 - 16:30:03 PDT
