On Mon, Dec 22, 2014, Nhai wrote:
> > tleap -f leaprc.ff99SB
> > source leaprc.gaff
> > LIG = loadmol2 $mol.mol2
> > loadamberparams $mol.frcmod
> > saveamberparm LIG $mol.prmtop $mol.inpcrd
> > quit
You can't do this inside a script. Just to make what other have suggested to
be more explicit:
cat <<EOF > leap.in
source oldff/leaprc.ff99SB
source leaprc.gaff
LIG = loadmol2 $mol.mol2
loadamberparams $mol.frcmod
saveamberparm LIG $mol.prmtop $mol.inpcrd
quit
EOF
tleap -f leap.in
Notes: I've used "oldff/leaprc.ff99SB" since ff99SB is an old force field,
and should only be used if you really sure that is what you need.
Consider using ff14SB instead.
...hope this helps....dac
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Received on Mon Dec 22 2014 - 14:30:03 PST
