On Tue, Jan 12, 2010, Alan wrote:
>
> I am using AT 1.3 (with sqm) in either Linux 64 (Debian 5.0 with gcc) and
> Mac OSX (10.6.2 with intel and intel mkl).
> /usr/local/amber11/bin/antechamber -i Bej.none_neutral.ideal.mol2 -fi mol2
> -o Bej.none_neutral.ideal_bcc_gaff.mol2 -fo mol2 -c bcc -nc 0 -m 1 -s 2 -df
> 2 -at gaff -pf n # may take more than an hour to run
Can you post your input mol2 file? We have not seen differences in am1-bcc
charges between mac and linux systems, but I am sure our test molecule set is
somewhat limited.
> The problem is that if run such commands in my Mac, the final net charge is
> 0.004 and tleap: check BEJ doesn't complain.
>
> But if I run on linux, net charge is 0.01 and then tleap prints:
Both of these are odd. There can be round-off errors because sqm only prints
Mulliken charges to three places after the decimal point. What is the
"Total Mulliken Charge" printed out in sqm.out? Once we know how large your
system is, it would be easier to know if these values could be from round-off
or not.
If you like, you can edit $AMBERHOME/src/sqm/qm2_print_charges.f, changing
lines 47 and 57 to give higher precision output.
You should also examine the sqm.out files to see if the geometry minimization
actually completed correctly on both computers. Be sure to read the note on
sqm tolerances:
http://archive.ambermd.org/201001/0078.html
...good luck...dac
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Received on Tue Jan 12 2010 - 07:00:02 PST
