Permission denied or command not found

Incidentally, you should not need to specify the full address of, if you put the directory
("/home/ali-pc/md/moltemplate/src/") in your PATH environment
variable. (This is discussed at the beginning of the moltemplate
manual. I assume you are using linux, mac, mingw, or cygwin)

To solve this problem, in your case, try adding these lines to your
~/.bashrc file, then log out, and log in again:
export PATH="$PATH:$HOME/md/moltemplate/src"
export MOLTEMPLATE_PATH="$HOME/md/moltemplate/common"

Anyway, regarding the permission-denied error message, it looks like
the file permissions were modified at some point. (This sometimes
happens if you temporarily copy the moltemplate directory to a hard
drive or memory stick formatted as NTFS, FAT, or HFS) To fix this,

--- fast (but not very reliable) solution ---

cd /home/ali-pc/md/moltemplate/src
chmod 755 *.sh *.py

--- thorough solution ---
The better way is to run chmod recursively this way:

cd /home/ali-pc/md/moltemplate/
find . -type d -exec chmod 755 {} \;
find . -type f -exec chmod 644 {} \;
find . -type f -name "*.sh" -exec chmod 755 {} \;
find . -type f -name "*.py" -exec chmod 755 {} \;

Hope this helps.