xleap to generate prmtop and inpcrd files

Now that we have the lib file with the information for all the molecules we need to include and also the corresponding combined pdb file, creating prmtop and inpcrd files should not be a difficult task.
So, to begin with we have

a lib file name: molecule.lib
a pdb file for 4 molecules name: four.pdb

The  task is to generate a prmtop and inpcrd file.

Initiate xleap using:

$AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99

In xleap window
> source leaprc.gaff

# load the lib file by:

> loadoff molecule.lib

I am not sure but some times it helps to also load the frcmod files we created for the four molecules the information of which is stored in the lib file.
> loadamberparams aldehyde.frcmod

# Load the pdb file:

> P=loadpdb four.pdb

You should see some thing like this in the xleap window now:
-------------------
> P=loadpdb four.pdb
Loading PDB file: ./four.pdb
Warning: name change in pdb file residue 1 ;
 this residue is split into NIT and ACE.
Warning: name change in pdb file residue 1 ;
 this residue is split into ACE and BZN.
Warning: name change in pdb file residue 1 ;
 this residue is split into BZN and HDX.
3 residues had naming warnings.
 There are split residues;
 residue sequence numbers will not correspond to those in the pdb.
  total atoms in file: 35
------------------

Now you have created a unit with name P where in your system is present.
You can check it using:
> list
This will give a list of all the units present in xleap. P will also be present in this list.

> edit P

will help to visualize the structure we loaded.

If everything is fine xleap should show the four molecules we wanted to club together as a single system.

We can save prmtop and inpcrd files for the system using

> saveamberparm P four.prmtop four.inpcrd
These are the two files we require while submitting any calculation for a system in amber.

We can also solvate the system at this point with say methanol solvent.

> solvatebox P MEOHBOX 8.0

The command creates a 8.0 Angstrom box full of methanol molecules  around our system.Save the topology(prmtop) and coordinate files(inpcrd) using:

> saveamberparm SUS solvated_four.prmtop solvated_four.inpcrd

The system is now ready for the MD simulations