Copy file(s) into specified directories

#!/bin/bash

shopt -s nullglob

cd home/Desktop/chain/file || exit 1

for name in ./*.pdb*; do
    for dir in "../${name%.pdb*}"*/; do
        cp "$name" "$dir"
    done
done

This would loop over all the PDB files in the home/Desktop/chain/file directory, with $name holding a name in each iteration. If you are certain that you only have a single character after .pdb at the end of the names, then the pattern ./*.pdb* should be changed to ./*.pdb?, and the pattern used in the parameter substitution in the inner loop should be changed accordingly.

For each file, the file would be copied to each of the directories corresponding to the name with the .pdb* suffix removed in the home/Desktop/chain directory (${name%.pdb*} is the name of the file with the suffix matching .pdb* removed). This is done in an inner loop.

The inner loop is necessary as it's not possible to use cp with multiple target directories, like you're trying to do.

Setting the nullglob shell option at the start ensures that a pattern is removed rather than retained unexpanded if it doesn't match anything.

Example (this shows the view of the chain directory)

$ tree -F
.
|-- 1b47_A/
|-- 1b47_B/
|-- 3rty_H/
|-- 7yt5_2/
|-- 7yt5_5/
|-- 7yt5_L/
`-- file/
    |-- 1b47.pdb1
    |-- 3rty.pdb1
    |-- 3rty.pdb3
    |-- 7yt5.pdb1
    |-- 7yt5.pdb2
    `-- 7yt5.pdb5

7 directories, 6 files

Loop is run here. The result:

$ tree -F
.
|-- 1b47_A/
|   `-- 1b47.pdb1
|-- 1b47_B/
|   `-- 1b47.pdb1
|-- 3rty_H/
|   |-- 3rty.pdb1
|   `-- 3rty.pdb3
|-- 7yt5_2/
|   |-- 7yt5.pdb1
|   |-- 7yt5.pdb2
|   `-- 7yt5.pdb5
|-- 7yt5_5/
|   |-- 7yt5.pdb1
|   |-- 7yt5.pdb2
|   `-- 7yt5.pdb5
|-- 7yt5_L/
|   |-- 7yt5.pdb1
|   |-- 7yt5.pdb2
|   `-- 7yt5.pdb5
`-- file/
    |-- 1b47.pdb1
    |-- 3rty.pdb1
    |-- 3rty.pdb3
    |-- 7yt5.pdb1
    |-- 7yt5.pdb2
    `-- 7yt5.pdb5

7 directories, 19 files

You could potentially save space by instead of copying the files create hard links. You would do this by simply changing cp to ln in the script.

You would not do this if you intend to modify the files in a directory independently of the files with the same name in other directories. A hard link is simply an additional name for a file.

You can do this without having nested loops:

cd home/Desktop/chain
for dir in *_?
do
        base=${dir%_?}
        cp  file/"$base".*  "$dir"
done

This assumes that there are no files under home/Desktop/chain whose names have a _ as the penultimate (second-to-last) character.  If there are, use

cd home/Desktop/chain
for dir in *_?/
do
        base=${dir%_?/}
        cp  file/"$base".*  "$dir"
done

in which we append / to the *_? pattern to get only directories.