AMBER Archive (2008)

Subject: Re: AMBER: N(CN2)- ion

From: babak minoofar (babak_minoofar_at_yahoo.com)
Date: Fri Dec 12 2008 - 03:29:54 CST

Dear David,
   With all the changes you proposed on last e-mail I go the same structer. Do you think that by changing constrain in bond, angel and dihedrals I can solve the problem or I should start to have proper force field from begining.
Regards
    Babak

________________________________
From: David A. Case <case_at_biomaps.rutgers.edu>
To: amber_at_scripps.edu
Sent: Friday, December 5, 2008 1:23:05 PM
Subject: Re: AMBER: N(CN2)- ion

On Thu, Dec 04, 2008, babak minoofar wrote:

> Thanks for e-mail. I used gaff force filed for MD. After doing ab intio
> calculations and get I got prep file qnd then I made lib file then I used
> gaff force field to produce prameters file but I got message which said
> there angle na dihedral are missing. n1-c1-ne, c1-n1-cg-n1 which I used
> similar parameters force constant from gaff and angle from ab initio
> like:
> type angle force constant
> n1-c1-ne 173 120

Sorry if I am misremembering, but wasn't your intial problem that the N-C-N
(terminal) group was not linear, but bent? If you have an angle term constant
with a minimum at 173, that would seem to explain that behavior.

> c1-n1-cg-n1 1.1 180. 2.0 like X - X - X -X

Can you describe which atoms have which types? I'm kind of surprised that you
have two types of carbons -- aren't both carbons equivalent?

> I got so strange behvior of N(CN2)- ion.

Actually, I am also assuming that you are really looking at N(CN)2- (three N
atoms, two C atoms) not "N(CN2)-", which would have three N and one C. So
you may need to clarify this.

If you assign atoms like this: ne-c-nc-c-ne, I think you will need to do
something like the following:

define an ne-nc "bond", with equilibrium distance at the linear ne-nc distance

set the ne-c-nc, nc-ne-c and c-nc-ne angles to zero force constant

set all dihedrals to zero force constant

(The reason for the this is that diehedrals won't work for linear bonds, so
you have to use the pseudo-bond ne-nc to maintain linearity.)

You'll have to do all this manually--antechamber won't handle system like this
automatically.

...good luck...dac

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