Thanks Prof.David. It works now. I will run this script for 200 ligand
files.
2014-12-22 23:13 GMT+01:00 David A Case <case.biomaps.rutgers.edu>:
> 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 - 15:30:02 PST
