Re: [AMBER] Force constant

From: William Flak <>
Date: Sun, 18 Apr 2010 09:56:53 -0700 (PDT)

Dear Dr. NicholasThank you for an instant reply.I did optimization (minimization) of two fragments (two separated molecules) using the previously posted input. When I changed the force constant for bond length between N and EP from 500 to 600 (just to test it) I found the minimized geometry changed, i.e. the bond distance between EP and H-second fragment. I couldn't see why, changing the force constant may affect on the total energy of one fragment, but why it affected  the electrostatic interaction and geometry.I used GAFF force field, where I minimized only two ligands (heterocyclic compounds).
I have more questions, if you don't mind please:* How they determined the force parameters for the lone pair in the original paper:RICHARD W. DIXON, PETER A. KOLLMAN "Advancing Beyond the Atom-Centered Model in Additive and Nonadditive Molecular Mechanics"* Should I set dihedral parameter for the EP to zero because it is missing?
Thank you in advance

--- On Sun, 4/18/10, Nicholas Musolino <musolino.MIT.EDU> wrote:

From: Nicholas Musolino <musolino.MIT.EDU>
Subject: Re: [AMBER] Force constant
To: "AMBER Mailing List" <>
Date: Sunday, April 18, 2010, 4:08 PM

On Apr 18, 2010, at 11:54 AM, William Flak wrote:
> Dear users
> I am trying to optimize two molecules interacting together using AMBER. The interaction takes place on a lone pair (treated as EP in AMBER).Minimization should be in gas phase, I used the following input file, could you check it? &cntrl  imin   = 1,  maxcyc = 1250,  ncyc   = 1000,  ntb    = 0,  ntr    = 0,  cut    = 999 /
> In fact, I got a weird data, if I changed the force constant for the bond length between EP and X from 500 to 600, the interaction between lone pair (on one fragment) and the other fragment completely changed. Why?Thanks

Dear William,
I don't think I'm experienced enough with AMBER to evaluate the details of your input file.

To evaluate the underlying physical/numerical issue, however, I think we'll need more information.  What do you mean when you say the "interaction completely changed"?  Do you mean the interaction energy, or the geometry? I agree with your implication that a drastic change would be unexpected.

Also important would be to understand which force field you're using, and how you're obtaining parameters for these molecules.  What kind of molecules are they?

Zooming out a bit, my instinct is to be cautious with lone pairs, as others have suggested on this list before (see 

If you write back with more info, we might be able to make more suggestions.  Best of luck,
Nicholas Musolino

PS.  Don't know if it's a mail client issue on your end or my end, but your e-mail came through with no line breaks, at least in my inbox.
Nicholas Musolino
Ph.D. candidate, Department of Chemical Engineering, MIT  |  617-253-6675  |  Room E19-528

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Received on Sun Apr 18 2010 - 10:00:02 PDT
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