Hello!
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
I get:
Info: the atom number exceeds the MAXATOM, reallocate memory automatically
Info: the atom number exceeds the MAXATOM, reallocate memory automatically
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
The atom number exceeds the MAXATOM, reallocate memory
I am not sure if the command was given correctly or there is some other
issue.
Sorry for getting back and forth on this, but all I need from Amber right
now is to assign partial charges to my mol2 file. I'd really appreciate some
help.
Thanks!
On Mon, Aug 30, 2010 at 5:28 PM, David A. Case <case.biomaps.rutgers.edu>wrote:
> On Mon, Aug 30, 2010, P Bhattacharya wrote:
>
> > Total number of electrons: 1852; net charge: 0
>
> This is a very large number of electrons, and sqm might take a *long* time.
> I suggest you try with much smaller molecules until you are familiar with
> antechamber.
>
> The order of flags does not matter on the command line.
>
> > The latter displays : antechamber: command not found
>
> You need to learn how to solve problems like this one on your own. See if
> a
> friend who knows Linux can walk you through what is going on, and/or work
> through a tutorial on Linux, to learn about environment variables, your
> PATH,
> and how command line invocation works.
>
> ...good luck...dac
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Priyanka Bhattacharya
PhD candidate
Laboratory of Single-Molecule Biophysics and Polymer Physics
Department of Physics and Astronomy, Clemson University
Lab: Jordan 110
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Received on Wed Sep 01 2010 - 13:30:04 PDT
