It says moltemplate.sh: command not found although I have got the
correct path. maybe I did something wrong again or maybe it is an
installation problem after all?
It definitely seems that way, but that does not guarantee that
moltemplate.sh has no errors.
It sounds like if you have limited time, you should find someone to
help you install this software (python 2.7, moltemplate and/or
lammps).
I imagine that trying to get python 2.7 installed on cygwin could be
difficult. I think it's easier to run moltemplate (and LAMMPS) on a
fresh linux installation. The latest version of ubuntu 12.04 (and the
newer 12.10 comming out in a few days) includes a new version of
python by default.
http://www.ubuntu.com/download/help/try-ubuntu-before-you-install
But this is just one possibility.
Also, you will find attached the PDB file of my polymer. I have decided to
send it to you instead of posting to the LAMMPS mailing list. If you do have
time, please just have a look at it and give me a general guidance and would
like to know how to quickly meddle with the data and input file in LAMMPS
(for the time being as I am really tight on time ).
Can you send me your .LT file as well?
If you don't feel comfortable sending me the true version, feel free
to change it before you send it to me.
Cheers and good luck.
Andrew
P.S.
Thanks Bruce for posting a more detailed description of Molecular
Dynamics Studio.