Subject: CCL: MOE - MMFF94s geometry and 9-6 van der Waals potential

From: Oliver Hucke <ohucke=at=u.washington.edu>
Date: Thu, 11 Mar 2004 13:29:50 -0800

Dear All,

I am using the program MOE to address a ligand docking problem.

During this work the following questions arose:

1. With the MMFF94s force field some of my small molecules show strange
geometries if I use force field charges. An example is the
4-cyano-anilin attached to this email. The aromatic ring is not really
planar and the substituents are far from being in plane of the ring!?
The problem seems to occur upon presence of the nitrogen. With MMFF94 I
obtain the same result.

Has somebody an explanation for the strange geometry obtained after
MMFF94(s) energy minimization?

2. I would like to use a 9-6 van der Waals potential. I figured out that
I need to adjust the parameters "Buffer1" and "Buffer2" in the
potential setup. Which values would I have to assign?

Your help is very much appreciated.

Best regards,
Oliver

-- 
_______________________________________________________________

Oliver Hucke, Dr.
                                Health Sciences Building - K418C
University of Washington      1959 NE Pacific St.
Dept. of Biochemistry         phone: (206) 685 7046
Box 357742                    fax  : (206) 685 7002
Seattle, WA 98195-7742        email: ohucke=at=u.washington.edu
_______________________________________________________________
HETATM    1  C8  SCH  2002     106.876  19.189  33.807        0.00           C  
HETATM    2  H   SCH  2002     107.539  18.490  34.313        0.00           H  
HETATM    3  C13 SCH  2002     106.222  18.802  32.656        0.00           C  
HETATM    4  H   SCH  2002     106.376  17.804  32.256        0.00           H  
HETATM    5  C15 SCH  2002     105.415  19.716  31.980        0.00           C  
HETATM    6  N2  SCH  2002     104.998  19.411  30.700        0.00           N  
HETATM    7  H   SCH  2002     104.152  19.917  30.398        0.00           H  
HETATM    8  H   SCH  2002     104.806  18.410  30.544        0.00           H  
HETATM    9  C9  SCH  2002     105.259  21.022  32.441        0.00           C  
HETATM   10  H   SCH  2002     104.669  21.737  31.876        0.00           H  
HETATM   11  C10 SCH  2002     105.907  21.423  33.591        0.00           C  
HETATM   12  H   SCH  2002     105.818  22.453  33.930        0.00           H  
HETATM   13  C11 SCH  2002     106.733  20.506  34.236        0.00           C  
HETATM   14  C   SCH  2002     107.564  20.967  35.270        0.00           C  
HETATM   15  N   SCH  2002     108.323  21.370  36.038        0.00           N  
CONECT    1    2    3   13
CONECT    2    1
CONECT    3    1    4    5
CONECT    4    3
CONECT    5    3    6    9
CONECT    6    5    7    8
CONECT    7    6
CONECT    8    6
CONECT    9    5   10   11
CONECT   10    9
CONECT   11    9   12   13
CONECT   12   11
CONECT   13    1   11   14
CONECT   14   13   15
CONECT   15   14
END