AMBER Archive (2009)

Subject: Re: [AMBER] sqm x mopac in AmberTools 1.3

From: David Watson (dewatson_at_olemiss.edu)
Date: Tue Dec 22 2009 - 09:20:37 CST

On Dec 22, 2009, at 9:02 AM, Alan wrote:

> 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
>

I believe when you use -macAccelerate it ignores MKL.

> 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!
>

I also notice longer antechamber times using sqm vs mopac.

MacBook, SL 10.6.2, Intel 11.076 compilers/MKL.
Compiled using
    ./configure intel
but there are two odd tests.

Namely,
--------
Running test to do simple lmod optimization

1c1
< Glob. min. E = -128.257 kcal/mol 

---
> Glob. min. E         =     -136.806 kcal/mol
   FAILED (probably OK if energy is -120 to -130)
--------

and

--------
cd DNA; ./Run.DNA1
diffing 132d.mol2.save with 132d.mol2
possible FAILURE:  check 132d.mol2.dif
--------

I'm not sure if the sleap test failure is a true failure or not, but I'll attach the diff anyway.


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