AMBER Archive (2009)

Subject: Re: [AMBER] trouble with antechamber

From: case (case_at_biomaps.rutgers.edu)
Date: Tue Nov 24 2009 - 14:41:24 CST

> From: Jordan Feigerle
> Sent: Tuesday, November 24, 2009 2:04 PM
> To: Jennifer L. Muzyka
>
> I am using Amber10 and I am having difficulties using antechamber to
> simulate an organic compound. I attempted to perform the tutorial with
> the sustiva.pdb file but my pc was not able to finish the calculations.
> My first question is how long is the calculation on a 32-bit 2.4 GHz PC
> using Ubuntu.

Depends on the size of the molecule you are using, but 1-5 minutes should be
plenty.

> My second question is regarding mopac. I had been having some of the
> problems other posters have had concerning the "&" in the mopac.sh code.

Be sure you have the latest version of AmberTools (1.2). There is no '&'
character in mopac.sh, at least that I can see. You might try to see how that
got there.

> shows that mopac is using 100% of the processor). The output file which
> mopac designates at FOR006 is created with the following message at the
> bottom: "NO POINT LOWER IN ENERGY THAN THE STARTING POINT COULD BE FOUND
> IN THE LINE MINIMIZATION."

Usual question (sorry if I missed this in earlier posts): do the test cases
work? Go to $AMBERHOME/test/antechamber/tp and type './Run.tp' Does this
work? Look at the mopac.out file for clues if bad things happen. But this
will narrow down whether this is a problem with the mopac program itself, or
with the input for your particular molecule.

...dac

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