CCL: Force field calculations-getting started

Hi Aaron,
Although I haven't extensively used FF calculations, I used Tinker for some tautomer/isomer search. Molden http://www.cmbi.ru.nl/molden/ can generate everything you need. 
Hope for the best.
Sincerely

Davor Sakic

Department of General and Inorganic Chemistry
Faculty of Pharmacy and Biochemistry, www.pharma.hr
University of Zagreb
Ante Kovacica 1
10000 Zagreb
Croatia
davor.sakic||gmail.com
dsakic||pharma.hr

On 11. sij. 2011., at 05:34, Alavi, Saman Saman.Alavi!A!nrc-cnrc.gc.ca wrote:

Hi Aaron,
 
You may want to look at DL_FIELD which is a new utility for constructing the FIELD file for use in DL_POLY. It is free of charge and only requires registration.
 
An alternative is to use the AMBER "antechamber" program to determine the atom types, count (and list) bounds between the atoms (and harmonic force constants between them,) angles and harmonic angle bend harmonic force constants, dihedrals (proper and improper) along with the related parameters, etc. according to the AMBER force field functions. Parameters for many types of potential (including OPLS) are available in AMBER. Once you get the list of bonds, angles, dihedrals > from the antechamber program, it is a much easier task to prepare the DL_POLY FIELD file. I can send a more detailed description of the procedure if you have access to AMBER and antechamber.
 
I hope this helps.
 
Best regards,
Saman Alavi
 
From: owner-chemistry+saman.alavi==nrc.ca{:}ccl.net [owner-chemistry+saman.alavi==nrc.ca{:}ccl.net] On Behalf Of Deskins, N Aaron nadeskins++WPI.EDU [owner-chemistry{:}ccl.net]
Sent: January-10-11 9:29 AM
To: Alavi, Saman
Subject: CCL: Force field calculations-getting started

Hello fellow CCL’ers,

 

  I find myself increasingly in need of running some force field calculations (e.g. OPLS) for organic/biological molecules, and am looking for the best way to get started. I come from an electronic structure background where making an input file is pretty straight-forward. Choose atomic coordinates (xyz), basis set, methodology, and run the calculation.

 

  Setting up an input file for the various molecular mechanics methods however seems more complicated. You can start with the xyz atomic coordinates, but you also have to worry about various atom types for the same element, atom connectivity, etc.

 

Can anyone suggest some software/website/tutorial that would help in setting up an input file?

 

    I’m leaning towards using DL_POLY (I have experience with this code for ‘simpler’ systems) with the OPLS force field, but this isn’t set in stone. OPLS seems to be widely used for the types of molecules I’m interested in (organics).

 

Thank you, 

 

N. Aaron Deskins
Assistant Professor
Chemical Engineering Department
Worcester Polytechnic Institute
Worcester, MA