1. Optimize BENZENE structure in Gaussian and calculate ESP

2. Use Antechamber in AMBERTOOLS to generate prep file (ben.prep)

3. Use parmchk in AMBERTOOLS to check the missing force field terms (ben.frcmod)

4. Use tleap in AMBERTOOLS

####This is the script for tleap###

source leaprc.gaff

loadamberprep ben.prep

loadamberparams ben.frcmod

ben = loadpdb ben.pdb

check ben

charge ben

saveamberparm ben ben.prmtop ben.inpcrd

quit

########################################

You may search ANTECHAMBER in Google for more detailed explanation.

And read this tutorial before you do this.

http://ambermd.org/tutorials/basic/tutorial4b/

1. Optimize BENZENE structure in Gaussian and calculate ESP

2. Use Antechamber in AMBERTOOLS to generate prep file (ben.prep)

3. Use parmchk in AMBERTOOLS to check the missing force field terms (ben.frcmod)

4. Use tleap in AMBERTOOLS

####This is the script for tleap###

source leaprc.gaff

loadamberprep ben.prep

loadamberparams ben.frcmod

ben = loadpdb ben.pdb

check ben

charge ben

saveamberparm ben ben.prmtop ben.inpcrd

quit

########################################

You may search ANTECHAMBER in Google for more detailed explanation.

And read this tutorial before you do this.

http://ambermd.org/tutorials/basic/tutorial4b/

check this out,

http://webapps.ccpn.ac.uk/acpype/

Antechamber is freely available to all. Just optimize ur structure in Jaguar/Guassian and use antechamber to get its topology. For antechamber commands n all just contact me directly.