Hello Tammy,
One thought is that you can use the mask keyword in cpptraj to generate a file. This file, call it mask.txt, will list the atom numbers in the second column. You then can process this file with a bash script to get a comma separated list, something like the following:
idx=0
while IFS= read -r F1 <&2;do
if [ $idx != 0 ];then
atnum=$(echo $F1 | awk '{print $2}')
echo -n “${atnum},";
fi
idx=$((idx+1))
done 2< mask.txt
Note that the line indexing (idx) is to skip the “AtomNum” header in mask.txt.
Hope this work-around helps.
Best,
Matthew
> On Jan 18, 2022, at 8:01 PM, Ming Tang <m21.tang.qut.edu.au> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> Dear list,
>
> Is there a command to print out atom indexes (separated by comma) for a large number of residues? I want to use them as cv_i in ABMD.
>
> Thanks,
> Tammy
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Received on Tue Jan 18 2022 - 19:30:02 PST
