cat a very large number of files together in correct order

Using find, sort and xargs:

find . -maxdepth 1 -type f -name 'file_*.pdb' -print0 |
sort -zV |
xargs -0 cat >all.pdb

The find command finds all relevant files, then prints their pathnames out to sort that does a "version sort" to get them in the right order (if the numbers in the filenames had been zero-filled to a fixed width we would not have needed -V). xargs takes this list of sorted pathnames and runs cat on these in as large batches as possible.

This should work even if the filenames contains strange characters such as newlines and spaces. We use -print0 with find to give sort nul-terminated names to sort, and sort handles these using -z. xargs too reads nul-terminated names with its -0 flag.

Note that I'm writing the result to a file whose name does not match the pattern file_*.pdb.

---

The above solution uses some non-standard flags for some utilities. These are supported by the GNU implementation of these utilities and at least by the OpenBSD and the macOS implementation.

The non-standard flags used are

• -maxdepth 1, to make find only enter the top-most directory but no subdirectories. POSIXly, use find . ! -name . -prune ...
• -print0, to make find output nul-terminated pathnames (this was considered by POSIX but rejected). One could use -exec printf '%s\0' {} + instead.
• -z, to make sort take nul-terminated records. There is no POSIX equivalence.
• -V, to make sort sort e.g. 200 after 3. There is no POSIX equivalence, but could be replaced by a numeric sort on specific parts of the filename if the filenames have a fixed prefix.
• -0, to make xargs read nul-terminated records. There is no POSIX equivalence. POSIXly, one would need to quote the file names in a format recognised by xargs.

If the pathnames are well behaved, and if the directory structure is flat (no subdirectories), then one could make do without these flags, except for -V with sort.

With zsh (where that {1..15000} operator comes from):

autoload zargs # best in ~/.zshrc
zargs file_{1..15000}.pdb -- cat > file_all.pdb

Or for all file_<digits>.pdb files in numerical order:

zargs file_<->.pdb(n) -- cat > file_all.pdb

(where <x-y> is a glob operator that matches on decimal numbers x to y. With no x nor y, it's any decimal number. Equivalent to extendedglob's [0-9]## or kshglob's +([0-9]) (one or more digits)).

With ksh93, using its builtin cat command (so not affected by that limit of the execve() system call since there's no execution):

command /opt/ast/bin/cat file_{1..15000}.pdb > file_all.pdb

With bash/zsh/ksh93 (which support zsh's {x..y} and have printf builtin):

printf '%s\n' file_{1..15000}.pdb | xargs cat > file_all.pdb

On a GNU system or compatible, you could also use seq:

seq -f 'file_%.17g.pdb' 15000 | xargs cat > file_all.pdb

For the xargs-based solutions, special care would have to be taken for file names that contain blanks, single or double quotes or backslashes.

Like for -It's a trickier filename - 12.pdb, use:

seq -f "\"./-It's a trickier filename - %.17g.pdb\"" 15000 |
  xargs cat > file_all.pdb

A for loop is possible, and very simple.

for i in file_{1..15000}.pdb; do cat $i >> file_all.pdb; done

The downside is that you invoke cat a hell of a lot of times. But if you can't remember exactly how to do the stuff with find and the invocation overhead isn't too bad in your situation, then it's worth keeping in mind.