Looks like you are putting tleap commands directly in the bash script,
instead of running them in tleap.
There are many ways in which you can handle this in a bash script (google
may be your friend there...).
A simple but tractable way would be to generate a tleap input script in
your bash script (e.g. tleap.in), and then run it in the script (tleap -f
tleap.in).
--Marc
On 22 December 2014 at 15:05, Ahmet yıldırım <ahmedo047.gmail.com> wrote:
>
> Dear users,
>
> I need to a bash script for Antechamber. Unfortunately my script doesn't
> work correctly. It stops after "tleap -f leaprc.ff99SB" step. Can anyone
> help me with this?
>
> myscript:
>
> #!/bin/bash
>
> mol=lig1
>
> antechamber -i $mol.log -fi gout -o $mol.mol2 -fo mol2 -c resp -nc 1 -rn
> LIG -at gaff -du n -an n -pf y
> parmchk -i $mol.mol2 -o $mol.frcmod -f mol2 -a Y
> tleap -f leaprc.ff99SB
> source leaprc.gaff
> LIG = loadmol2 $mol.mol2
> loadamberparams $mol.frcmod
> saveamberparm LIG $mol.prmtop $mol.inpcrd
> quit
>
> --
> Ahmet Yıldırım
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> AMBER.ambermd.org
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>
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Received on Mon Dec 22 2014 - 09:00:04 PST
