From owner-chemistry@ccl.net Mon Jan 10 23:37:00 2011 From: "Alavi, Saman Saman.Alavi!A!nrc-cnrc.gc.ca" To: CCL Subject: CCL: Force field calculations-getting started Message-Id: <-43596-110110233424-24391-dNE3NGwe0JO6veqr1QVh3A#server.ccl.net> X-Original-From: "Alavi, Saman" Content-Language: en-CA Content-Type: multipart/alternative; boundary="_000_001A8CD833A9894A8AED786976F90024024029E013NRCCENMB1nrcc_" Date: Mon, 10 Jan 2011 23:34:10 -0500 MIME-Version: 1.0 Sent to CCL by: "Alavi, Saman" [Saman.Alavi###nrc-cnrc.gc.ca] --_000_001A8CD833A9894A8AED786976F90024024029E013NRCCENMB1nrcc_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Hi Aaron, You may want to look at DL_FIELD which is a new utility for constructing th= e FIELD file for use in DL_POLY. It is free of charge and only requires reg= istration. http://www.cse.scitech.ac.uk/ccg/software/DL_FIELD/index.shtml An alternative is to use the AMBER "antechamber" program to determine the a= tom types, count (and list) bounds between the atoms (and harmonic force co= nstants between them,) angles and harmonic angle bend harmonic force consta= nts, dihedrals (proper and improper) along with the related parameters, etc= . according to the AMBER force field functions. Parameters for many types o= f potential (including OPLS) are available in AMBER. Once you get the list = of bonds, angles, dihedrals from the antechamber program, it is a much easi= er task to prepare the DL_POLY FIELD file. I can send a more detailed descr= iption of the procedure if you have access to AMBER and antechamber. I hope this helps. Best regards, Saman Alavi ________________________________ > From: owner-chemistry+saman.alavi=3D=3Dnrc.ca:_:ccl.net [owner-chemistry+sama= n.alavi=3D=3Dnrc.ca:_:ccl.net] On Behalf Of Deskins, N Aaron nadeskins++WPI.E= DU [owner-chemistry:_:ccl.net] Sent: January-10-11 9:29 AM To: Alavi, Saman Subject: CCL: Force field calculations-getting started Hello fellow CCL=92ers, I find myself increasingly in need of running some force field calculatio= ns (e.g. OPLS) for organic/biological molecules, and am looking for the bes= t 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 howe= ver 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, a= tom connectivity, etc. Can anyone suggest some software/website/tutorial that would help in settin= g up an input file? I=92m leaning towards using DL_POLY (I have experience with this code f= or =91simpler=92 systems) with the OPLS force field, but this isn=92t set i= n stone. OPLS seems to be widely used for the types of molecules I=92m inte= rested in (organics). Thank you, N. Aaron Deskins Assistant Professor Chemical Engineering Department Worcester Polytechnic Institute Worcester, MA http://users.wpi.edu/~nadeskins --_000_001A8CD833A9894A8AED786976F90024024029E013NRCCENMB1nrcc_ Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable

Hi Aaro= n,

You may want to look at D= L_FIELD which is a new utility for constructing the FIELD file for use in D= L_POLY. It is free of charge and only requires registration.

http://www.cse.scitech.ac= .uk/ccg/software/DL_FIELD/index.shtml

An alternative is to= use the AMBER "antechamber" program to determine the atom t= ypes, count (and list) bounds between the atoms (and harmonic for= ce constants between them,) angles and harmonic angle bend harmonic force constants, dihedrals (proper and improper) along with the related pa= rameters, etc. according to the AMBER force field functions. Parameter= s for many types of potential (including OPLS) are available in A= MBER. Once you get the list of bonds, angles, dihedrals from the antechamber program, it is a much easier task to prepare the DL_P= OLY FIELD file. I can send a more detailed description of the procedur= e if you have access to AMBER and antechamber.

I hope this helps.=

Best regards,

Saman Alavi

From: owner-chemistry+saman.ala= vi=3D=3Dnrc.ca:_:ccl.net [owner-chemistry+saman.alavi=3D=3Dnrc.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

He= llo fellow CCL=92ers,

&n= bsp;

&n= bsp; I find myself increasingly in need of running some force field ca= lculations (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 calc= ulation.

&n= bsp; Setting up an input file for the various molecular mechanics meth= ods however seems more complicated. You can start with the xyz atomic coord= inates, but you also have to worry about various atom types for the same element, atom connectivity, etc.

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

&n= bsp; I=92m leaning towards using DL_POLY (I have experience wit= h this code for =91simpler=92 systems) with the OPLS force field, but this = isn=92t set in stone. OPLS seems to be widely used for the types of molecules I=92m interested in (organics).

Th= ank you,

N. Aaron Deskins

Assistant Professor

Chemical Engineering Department

Worcester Polytechnic Institute

Worcester, MA

http://users.wpi.edu/~nadeskins

--_000_001A8CD833A9894A8AED786976F90024024029E013NRCCENMB1nrcc_--