[AMBER] sqm x mopac in AmberTools 1.3

From: Alan <alanwilter.gmail.com>
Date: Tue, 22 Dec 2009 15:02:22 +0000

Dear all,

I am very happy with AmberTools 1.3.

Nevertheless, I would like to clarify some questions.

I use MBP with SL 10.6.2 64 bits.

I compiled AT 1.3 as:

export MKL_HOME=/opt/intel/Compiler/11.1/076/Frameworks/mkl
./configure -macAccelerate intel
make -f Makefile_at
cd $AMBERHOME/test; make -f Makefile_at test

All Tests OK.

Then I tested antechamber on a ligand with sqm and mopac (which I just
copied mopac and mopac.sh from amber10/bin into amber11/bin):

First: with mopac, I got things done in 1min 20 s, with sqm it did in 15m 20
s. Yes, 14 min more!

The results for partial charges were almost identical.

I still have to test with some other ligands and in Linux 64 (where I have
problems with mopac, so I hope sqm will be fine).

Mopac saves a file mopac.pdb which is an optimised structure. Does sqm do
the same? How?

Well, many thanks for this new distribution. Pretty smooth (although long)
to compile and to install.

Happy Holidays,

Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org/
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)
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Received on Tue Dec 22 2009 - 07:30:03 PST
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