We have Amber10 in our lab. So this command won't work for that? Can you
please help me what else should I follow for Ligand-protein docked complex
simulation?
On Fri, May 11, 2012 at 5:03 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Fri, May 11, 2012, Asma Abro 28-FBAS/MSBI/F09 wrote:
> >
> > I have a problem regarding antechamber when I run this command:
> >
> > antechamber -i minlig_h.pdb -fi pdb -o lig.prepin -fo prepi -c bcc -s 2
> >
> > I get the following error:
> >
> > Running: /home/asma/AAData/AMBER/amber10//bin/sqm -O -i sqm.in -o
> sqm.out
> > sh: /home/asma/AAData/AMBER/amber10//bin/sqm: No such file or directory
>
> You don't have the sqm program installed, which makes sense since I don't
> think sqm was available in Amber10. It looks like your $AMBERHOME
> environment
> variable is wrong(?). It should point to a directory tree headed by
> "amber12"
> (for the current release), or maybe "amber11" if you are using an older
> version of AmberTools. See if that helps.
>
> ...dac
>
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Received on Fri May 11 2012 - 08:30:03 PDT
