http://ambermd.org/antechamber/ac.html#antechamber



Let's make the "file containing the atomic charges". 

antechamber -i 1EDN-h.pdb -fi pdb -o 1EDN.mol2 -fo mol2 -c AM1-BCC 


Then, I will convert the MOP form is a form of MOPAC input from PDB. 
sudo apt-get-y install openbabel 
babel -i pdb 1EDN.pdb -o mop 1EDN.mop -h 


It was named after seem to say say 
	1EDN.charge but, 
let's name them whatever you like so good. 

In mol2 format is a "file format that contains the atomic charges" to convert from using the antechamber. 
You will get tired of getting tired just conversion, but this is also fate. 

antechamber -i 1EDN.out -fi mopout -o 1EDN.mol2 -fo mol2 -c rc -cf 1EDN.charge -s 2 

1EDN.mol2 file is now available. Check the contents once, keep a look or lucky (number of far right) atomic charges. 
I will supplement the parameter was missing then. 
Use frcmod the (force field modification) in traditional as extension, 
but it does not matter because this is also easy to understand. 
AMBER because it is a great deal of freedom in the extension basis. 

parmchk -i 1EDN.mol2 -f mol2 -o 1EDN.frcmod 


I will convert to GROMACS for the topology file of AMBER for in the same way as before. 
think you need to pass through amb2gmx is easy, but let's specify the direct amb2gmx.pl If you are not through. 

amb2gmx -prmtop 1EDN.prmtop -crd 1EDN.crd -outname littlebusters 
