Subject: Re: CCL:programs to extract md needed force constants from g98 calculation

From: Per-Ola Norrby <[email-masked]>
Date: Mon, 22 Apr 2002 07:16:46 +0200

Hi,

>I'm trying to write a force parameter file for a inhibitor with sulfite
>substituents. Since the major force fields do not have them, I use g98 to
>generate the force constants. I wonder if there are any softwares that
>can change g98 output into the md format force constants. Thanks!

	Not completely straightforward, has to be done in a way that 
is compatible with the existing parts of the force field.  Have a 
look at:

"Automated Molecular Mechanics Parameterization with Simultaneous 
Utilization of Experimental and Quantum Chemical Data"
Per-Ola Norrby and Tommy Liljefors, J. Comput. Chem. 1998, 19, 1146-1166

"Deriving Force Field Parameters for Coordination Complexes"
Per-Ola Norrby and Peter Brandt, Coord. Chem. Rev. 2001, 212, 79-109

"Recipe for an organometallic force field"
Per-Ola Norrby, in Computational Organometallic Chemistry, Ed: T. 
Cundari; Marcel Dekker: New York, 2001, 7-37

	There are also numerous citations in these (in particular in 
the CCR review), to work dealing with general force field 
parameterization, by Hagler, Halgren, Rasmussen, Allinger, Dillen, ...

	Regards,

	Per-Ola
-- 

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Per-Ola Norrby, Assoc. Professor, http://compchem.dfh.dk/PeO/
Technical University of Denmark, Dept. of Chem., Org. Chem.
Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark
Email: [email-masked]  tel +45-45252123,  fax +45-45933968

---

From: Praveen M Bahadduri <[email-masked]>
Date: Mon, 22 Apr 2002 08:28:34 -0400

Hi! CCL,

I am working with autodock for some time. I had a recurring problem. I am
reposting this question.

When I run autodock program and read the docked pdb file in sybyl window, I get
a bunch of straight lines with dots. I cannot figure out if there is any
specific arrangement of these lines or dot. I carried it several times, but in
vain.

Can anybody please let me know solution to this problem?

Sincerely

Praveen

The Ohio-State University
Columbus, OH.