Hi,
You were close!. The command for closing out a loop block is 'done',
not 'do'. However, I wouldn't go about it this way since with 'trajin'
+ 'trajout onlyframes' you will be reading the entire input trajectory
each time. Here is a script that will extract all the frames from a
trajectory using trajin (so you will only read the single frame you
want to process) and write them out as single trajectories:
parm ../tz2.parm7
trajin ../tz2.nc
# Set N to the total number of frames in the trajectory
set N = trajinframes
for i=1;i<=$N;i++
# Clear the previous trajectory
clear trajin
# Read in a single frame
trajin ../tz2.nc $i $i
# Write it out
trajout temp.$i.nc
# Run
run
done
Hope this helps,
-Dan
On Sun, Oct 1, 2023 at 3:57 PM VERONICA MARTIN HERNANDEZ via AMBER
<amber.ambermd.org> wrote:
>
> Hi everyone again (and sorry for writting to much)
>
> I've to extract all the frames of a dynamic in separated files and I was trying with cpptraj and the following loop:
>
> parm CRBN-LVR-solv.prmtop
> trajin CRBN-LVR-NVTcenter.mdcrd
> for iFrame in {1..500}
> trajout CRBN-LVR-\$iFrame.mdcrd onlyframes \$iFrame
> do
> run
>
> But I get the following error:
>
> INPUT: Reading input from 'extract.in'
> [parm CRBN-LVR-solv.prmtop]
> Reading 'CRBN-LVR-solv.prmtop' as Amber Topology
> Radius Set: H(N)-modified Bondi radii (mbondi2)
> [trajin CRBN-LVR-NVTcenter.mdcrd]
> Reading 'CRBN-LVR-NVTcenter.mdcrd' as Amber Trajectory
> [for iFrame in {1..500}]
> Setting up 'for' loop.
> CONTROL: Parsing control block.
> BLOCK 0: for ((iFrame in {1..500})) do
> [trajout CRBN-LVR-\$iFrame.mdcrd onlyframes \$iFrame]
> Added command 'trajout' to control block 0.
> [do]
> Added command 'do' to control block 0.
> Error: 1 unterminated control block(s) detected.
> Error: 0 : for ((iFrame in {1..500})) do
> TIME: Total execution time: 0.1296 seconds.
> Error: Error(s) occurred during execution.
>
> How can I fix it?
> Thanks in advance
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Sun Oct 01 2023 - 18:00:02 PDT
