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Using Packmol

Packmol is a software that allows you to generate a single combined PDB file for all the molecules you are considering.
It is a free software and can be downloaded from this link:

http://www.ime.unicamp.br/~martinez/packmol/

The installation guide is also provided on the page and its really easy to follow.http://www.ime.unicamp.br/~martinez/packmol/

You can also find some examples but I tried on my own.
Anyway what you need is an input file which looks like:

------------------
tolerance 2.0
output trial.pdb
add_amber_ter
filetype pdb
structure 2a.pdb
  number 1
  inside cube 0. 0. 0. 10.
end structure
structure 2d.pdb
  number 1
  inside cube 0. 0. 0. 10.
end structure
---------------------------------

IT includes some information like:
how close the molecules considered can be.(tolerance)

name of output pdb file
"add_amber_ter" adds term "TER" after every molecule thus defining the start and end of every molecule.
After mentioning the filetype it has information of the input pdb files.
You can add as many different molecules here.
If you want repeating unit of same molecule then just mention information of one molecule and change the number setting from 1 to n, n is the number of units of that molecule.

I am showing here and example with pdb files of 2 molecules to be merged into one single PDB file.Name of the input file is trial.inp and output will be trial.pdb

you can execute packmol using command:

./packmol < trial.inp

You might require to launch packmol from its home directory packmol.
Sometimes I use command like:

../../../packmol/./packmol < trial.inp

The output is trial.pdb file that contains information of both the molecules.
Here is the output:

-----------------
HEADER
TITLE     Built with Packmol
REMARK   Packmol generated pdb file
REMARK   Home-Page: http://www.ime.unicamp.br/~martinez/packmol
REMARK
ATOM      1  C   NIT A   1       1.042   7.542   8.196  1.00  0.00
ATOM      2  N   NIT A   1       2.161   7.815   8.002  1.00  0.00
ATOM      3  C1  NIT A   1       3.530   8.137   7.761  1.00  0.00
ATOM      4  H   NIT A   1       4.155   7.317   8.121  1.00  0.00
ATOM      5  H1  NIT A   1       3.785   9.052   8.302  1.00  0.00
ATOM      6  H2  NIT A   1       3.683   8.275   6.691  1.00  0.00
TER
ATOM      7  OH  HDX B   1       0.527   9.826   9.789  1.00  0.00
ATOM      8 1HH  HDX B   1       0.526   8.877   9.941  1.00  0.00
ATOM      9 2HH  HDX B   1       0.536   9.998   8.845  1.00  0.00
TER
END

--------------------

You will get such a pdb file if you have generated your input pdb files by the method mentioned in previous posts. Check the unit names "NIT" and "HDX".
If your final pdb file appears like this, then it will compatible to the lib file you generated earlier. Otherwise you will landup with errors while try to load it on xleap later on.
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