AMBER: How do I make and enter new ff parameters into AMBER

From: HL Eastwood <>
Date: Fri, 02 Feb 2007 21:26:46 +0000

Dear Mary

I cannot fathom from your explanation whether the parameters you
require have been established or not. If they haven't been, I'm not the
dude to talk to. If they have been it's a fairly straightforward

1. start xleap.
2. load the force field parameter file that you wish to use (e.g
"source leaprc.ff03")
3. Type "list" and identify the name of the parameter file (this should
look like "parm.dat" or something similar).
3. Edit the parameter set by typing "edit" followed by the name of the
parameter file (e.g. "edit parm99.dat").
4. This will bring up a window that contains parameters that can be
altered manually. You will need to create a new entry for the atom
you're looking at and then specify all the parameter information such
as bond force constants, dihedral force constants etc (and charge if
you've performed a RESP fit on it). This will need to be done for each
connectivity that exists in the structure you're examining (I have no
idea what kind of system you're looking at but I'm guessing at this
stage that it will be coordinated in some way to other atoms).

I hope that helps!

hayden eastwood

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Received on Sun Feb 04 2007 - 06:08:03 PST
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