Unfortunately i couldn't find useful something on google. Maybe you can
send me a few web links about this topic. Yes, i putted the tleap commands
directly in the bash script. Because I dont know how to run in the tleap
the following commands. I am in tleap by using the bash script but i dont
know how to run the other commands in the tleap.
source leaprc.gaff
LIG = loadmol2 $mol.mol2
loadamberparams $mol.frcmod
saveamberparm LIG $mol.prmtop $mol.inpcrd
quit
Thanks in advance
2014-12-22 17:45 GMT+01:00 Marc van der Kamp <marcvanderkamp.gmail.com>:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Ahmet Yıldırım
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Received on Mon Dec 22 2014 - 10:30:05 PST
