Re: [AMBER] Execution Trouble

From: ankita mehta <>
Date: Fri, 18 Jun 2021 08:37:40 +0530

I mean running the following command :

*mpirun -np 2 pmemd.MPI -O -i <> -o
equil_1.out -p var_3.prmtop -c var_3.inpcrd -r var_equil_3.restart*

*takes time *

*so when cpptraj runs , it simply says var_equil_3.restart is not found.*

*Actually we want to automate this by scripting so , i need the ways to
avoid this.*

*IF I manually runs the scripts , everything works fine.*

*But how do i automate ?*

*Is there any way in scripting to wait while simulation is being run and
var_equil_3.restrst is completely written and then cpptraj should run.*

*P.S. i need to submit it in the nodes on the cluster. So, there is waiting
time at times.*


On Wed, Jun 16, 2021 at 6:16 PM David A Case <> wrote:

> On Wed, Jun 16, 2021, ankita mehta wrote:
> >*system "cpptraj -i <>";*
> It's hard to know what the exact command was that you used, since something
> (your mail program, you yourself?) added the http part. Did you get any
> error messages? Is the http part really there?
> >*So cpptraj command doesn’t run .*
> Just saying "doesn't run" is very vague, and doesn't allow anyone to offer
> help. Did you get any error messages? What happens if you run the cpptraj
> command at the console (i.e. without the perl part)?
> ....dac
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Received on Thu Jun 17 2021 - 20:30:02 PDT
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