Enim - amber

# Check the parameters not included

parmchk -i case.prep -f prepi -o case.frcmod
parmchk -i case.mol2 -f mol2 -o case.frcmod

# Check in mol2 file whether the total charge is the expected one:
 
cat case_RESP.mol2 | awk '{ sum+=$9} END {print sum}'
1.9996
# Add the remaining charge to be equal to 2.00


# Observe that gaff does not recognize Copper atom

more $AMBERHOME/dat/leap/parm/gaff.dat

# Check the parameters not included in the frcmod file

This command provides a frcmod file:

remark goes here
MASS
Cu 63.6                       ATTN, need revision


NONBON
  Cu          1.2000  0.0500  ATTN, need revision



Run leap


tleap -f leaprc.ff99SB
source leaprc.gaff

LIG = loadmol2 case.mol2
loadamberparams case.frcmod
saveoff LIG case.lib
saveamberparm LIG case.top case.inpcrd

addions LIG Cl- 0
saveoff LIG case_CI.lib
saveamberparm LIG case_CI.top case_CI.inpcrd

solvatebox LIG TIP3PBOX 14
saveoff LIG case_solv.lib
saveamberparm LIG case_solv.top case_solv.inpcrd



tleap -f leaprc.gaff
source leaprc.ff99SB
loadamberprep case.prep




5) Run sander

mpirun -np 8 sander.MPI -O -i min1.in -o min1.out -p case_solv.top -c case_solv.inpcrd -r case_solv_min1.rst -ref case_solv.inpcrd &


mpirun -np 8 sander.MPI -O -i min2.in -o min2.out -p case_solv.top -c case_solv_min1.rst -r case_solv_min2.rst &

mpirun -np 8 sander.MPI -O -i md1.in -o md1.out -p case_solv.top -c case_solv_min2.rst -r case_solv_md1.rst -x case_solv_md1.mdcrd -ref case_solv_min2.rst &


mpirun -np 8 sander.MPI -O -i md2.in -o md2.out -p case_solv.top -c case_solv_md1.rst -r case_solv_md2.rst -x case_solv_md2.mdcrd &

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