On Wed, Sep 01, 2010, P Bhattacharya wrote:
>
> Thanks for your suggestions. While I am getting acquainted with Linux
> gradually, although I know a little, I started with AmberTools. For the file
> I mentioned before, after running the antechamber command:
> $AMBERHOME/exe/antechamber -i Hyperbranched.mol2 -fi mol2 -o hb.mol2 -fo
> mol2 -c bcc
>
> Total number of electrons: 1852; net charge: 0
>
> Running: /home/pu-chunke/Priyanka/Amber/amber11/bin/sqm -O -i sqm.in -o
> sqm.out
>
> After 1.5 days, here's what I get:
>
> Error: cannot run "/home/pu-chunke/Priyanka/Amber/amber11/bin/sqm -O -i
> sqm.in -o sqm.out" of bcc() in charge.c properly, exit
This is a very large number of electrons. You can look at the "sqm.out"
file referred to above to get some idea of what problems antechamber saw.
It may be that you just need to loosen the convergence criteria -- see
Note 6 on p. 84 of the AmberTools users' manual. But my guess is that you
may have to use a smaller molecule if you want am1-bcc charges. It's hard
to say without knowing what your molecule is. Certainly, you should make sure
you can run antechamber on smaller systems, and are familiar with the contents
of the sqm.out file.
....dac
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Received on Wed Sep 01 2010 - 14:30:04 PDT
