Dear Dr. Case,
thank you for your response! The main issue why I've decided to switch from
sqm is that the topology with not integer charge was producing during
parametrization of large ligand (~60 atoms). In my research I deal with the
horomone-like ligands of membrane receptors. What method of charge
computations would be best suitable for the parametrization of such
molecules for amber force fields?
JAmes
2013/4/15 David A Case <case.biomaps.rutgers.edu>
> On Sat, Apr 13, 2013, James Starlight wrote:
> >
> > I'd like to use -q mopac flaq for charge assignment of my ligands.
> > I have installed mopac7 with the exe files /usr/bin/run_mopac7
> > in the antechamber's folder I've found mopac.sh where I've changed that
> > paths. Unfortunatelly when I've tried to use mopac in antechamber I've
> > obtained the error that mopac has not been installed.
>
> We need more information: which version of antehcamber? What is the exact
> antechamber command line, and the exact error message. (I don't see
> anything
> error messages that contain "installed"....)
>
> You'll probably have to do some debugging yourself here: we haven't used
> mopac in many years, and the option to request it may have become stale.
> But
> still, we need details about what you tried and what happened. Putting
> mopac into /usr/bin may not work (I'm guesing the antechamber looks in
> $AMBERHOME/bin. I don't remember ever having antehcamber using a file
> called
> run_mopac7....I think "mopac.sh" has always been the entry point--certainly
> amber/antechamber has never (at least officially) supported mopac7.
>
> So: are you sure you need to do this? If sqm is causing problems, it
> might be
> more productive to report those.
>
> ...dac
>
>
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Received on Mon Apr 15 2013 - 22:00:03 PDT
