Re: [AMBER] error

From: Gustaf Olsson <>
Date: Thu, 9 Jan 2020 06:54:22 +0000

Jumping in without having reviewed the previous posts.

Is your input spaced across multiple lines in your input file or is this just for readability?
You have multiple spaces between flags and options in you input, these should be removed.

These are minor things that sometimes causes read errors during execution and might be a problem.

-c ./vcte/smp-193ptn_vcon3.mdcrd

Should likely be a restart or input coordinates file (ncrst/rst/inpcrd) and not a mdcrd file? I am not sure as I have never tried it though I would also assume that

-ref ./vcte/smp-193ptn_vcon3.mdcrd

Should also be a restart/coordinates file and not a mdcrd file. Though both these options might work with trajectory data as well, have not tried it though.

If this is a simulation run (data production) and not an evaluation run you should not use with cpptraj. If you need to produce RST files (as these seems to be missing) then you use cpptraj to produce the missing files (references, from frames you deem reasonable) and use these in the script to produce data. Assuming that you remove double spaces and have the correct paths to premed.MPI and you I/O files, the script should be executed as:

chmod u+x

Regarding running cpptraj to produce RST files, you can do this interactively bu just running cpptraj and enter the correct commands, do this directly on the command line if you have the appropriate flags or create an input file and run as cpptraj -i input file.ptraj

Best regards
// Gustaf

On 8 Jan 2020, at 16:07, MYRIAN TORRES RICO <<>> wrote:

srun /gpfs/apps/NVIDIA/K80/AMBER/14/bin/pmemd.MPI -O -i
./min-tar/ -p ./leap/<> -c
./vcte/smp-193ptn_vcon3.mdcrd -r ./min-tar/smp-193ptn_min_wat.rst -o
./min-tar/smp-193ptn_min_wat.out -inf
./min-tar/<> -e ./min-tar/smp-193ptn_min_wat.enr
 -ref ./vcte/smp-193ptn_vcon3.mdcrd

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Received on Wed Jan 08 2020 - 23:00:02 PST
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