Hello all,
Please disregard the previous message. The error I made was trivial (i.e.,
there was a space present at the end of the -p line directly preceeding
line 22). I wound up finding it by checking every character in the text
against another functioning script from an AMBER MD tutorial.
Also, I found that pmemd.CUDA was not compatible with my heating and
equilibration steps, so converting those back to sander.MPI solved some
other unrelated errors with my code. Another issue is that I attempted to
use ntp > 0 for my implicit solvent equilibration step, which forces ntb >
0 (not compatible with implicit solvent to the best of my knowledge). I am
leaving these notes in case another inexperienced AMBER user such as myself
ends up with these issues.
All the best,
NDB
On Wed, Mar 30, 2022, 3:05 PM Nathan Black <nathanblack262.gmail.com> wrote:
> Hello AMBER Users,
>
> When running an MD Simulation on AMBER 20 using pmemd.cuda, the following
> error is given:
>
>
>
>
>
> *Unit 9 Error on OPEN: inpcrd
>
>
> STOP PMEMD Terminated
> Abnormally!./simulate_TEST2_AMBER20_GPU1: line 22: -c: command not foundAt
> line 857 of file /usr/local/amber20_src/src/pmemd/src/mdin_ctrl_dat.F90
> (unit = 5, file = 'TEST2_simulate.in')Fortran runtime error: Integer
> overflow while reading item 0*
>
> From my own experience and looking at other posts made to this mailing
> list, it initially appeared as though my inline tabs (used to "stretch" the
> command over multiple lines) are incorrect. However, I believe that they
> are (my script and its dependencies are attached). Also, using the
> pmemd.cuda -help command gave
>
>
>
> *usage: pmemd [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
> [-ref refc -x mdcrd -v mdvel -frc mdfrc -e mden -inf mdinfo -l
> logfile] [-amd amdlog_name -gamd gamdlog_name -scaledMD
> scaledMDlog_name -suffix output_files_suffix]*
>
> Which matches my input. I have attached my pmemd.cuda script and its
> dependencies, which were all in the same directory with reading
> permissions. From the error message that was given, I believe that the
> error is syntax-based and lies within the executable
> *simulate_TEST2_AMBER20_GPU1*, though I am admittedly lost on diagnosing
> it further.
>
> Any help is much appreciated. Thank you all for your continued support,
> NDB
>
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Received on Thu Mar 31 2022 - 07:00:02 PDT
