Subject: Problem with Macromodel on IRIX

From: Bruno Bienfait <[email-masked]>
Date: Thu, 08 Jul 1999 12:14:52 -0400

Dear CCL'ers,

I am using Macromodel 6.0  on several SGI workstations.  Surprisingly,
the results obtained on a SGI Octane with IRIX 6.4  were different from
those calculated on a Octane and an Origin both running  IRIX 6.5.

For instance, calculating the energy of cyclohexane (simply built using
the GUI) afforded the following results (force field = MMFF, solvent
=water):

IRIX 6.4 machine:

ENERGY:       37.03 kJ/mol (        8.85 kcal/mol)
Stretch:          15.62  Bend:               2.97
Prop Torsion:    -11.85  Improp Torsion:     0.00
Electrostatic:     0.00  Cross Terms:       -1.39
van der Waals:    24.17  Solvation:          7.50
Monitored BatchMin job completed.

two IRIX 6.5 machines:

ENERGY:        1.02 kJ/mol (        0.24 kcal/mol)
Stretch:          15.62  Bend:               2.97
Prop Torsion:    -47.86  Improp Torsion:     0.00
Electrostatic:     0.00  Cross Terms:       -1.39
van der Waals:    24.17  Solvation:          7.50
Monitored BatchMin job completed.

I observed similar differences using the MM3* force field without
solvent:

IRIX 6.4 machine:

ENERGY:       63.79 kJ/mol (       15.25 kcal/mol)
Stretch:           1.64  Bend:               0.42
Prop Torsion:     36.99  Improp Torsion:     0.00
Electrostatic:     0.00  Cross Terms:        0.08
van der Waals:    24.65  Solvation:          0.00
Monitored BatchMin job completed.

two IRIX 6.5 machines:

ENERGY:       33.93 kJ/mol (        8.11 kcal/mol)
Stretch:           1.64  Bend:               0.42
Prop Torsion:      7.13  Improp Torsion:     0.00
Electrostatic:     0.00  Cross Terms:        0.08
van der Waals:    24.65  Solvation:          0.00
Monitored BatchMin job completed.

I suppose that the differences observed  might be related to different
shared librairies.
Has anyone encountered such a problem before? Could someone confirm
which one of the two output is the correct one?

Thanks in advance.

Bruno

--
[ Bruno Bienfait, Ph. D.            Laboratory of Medicinal Chemistry ]
[                                   National Cancer Institute         ]
[ Email : [email-masked]      National Institutes of Health     ]
[ Phone : (301) 402-3111            Building 37, Room 5B20            ]
[ Fax   : (301) 496-5839            Bethesda Maryland 20892 , USA     ]
[ WWW   : http://www.brunob.org                                       ]

---

From: Peter Shenkin <[email-masked]>
Date: Thu, 8 Jul 1999 12:07:04 -0400 (EDT)

Hi,

There is a bug in the -mips4 fast math library (libfastm.so) originally 
distributed with IRIX 6.4 (and 6.3).  This can be fixed by upgrading to 
IRIX 6.5, or by installing patch Patch 1774 or 3131 & 3219, or 2752. (Some of 
these may superceded;  if so, install the later one(s).  But
your best bet is to upgrade.

BTW, this is Q4.4 on our FAQ page,  
	http://www.schrodinger.com/MacroModel/faq.html

Hope this helps,
-P.

--
********* Peter S. Shenkin; Schrodinger, Inc.; (201)433-2014 x111 *********
*********** [email-masked]; http://www.schrodinger.com ***********