AMBER Archive (2006)

Subject: Re: AMBER: Two different HIS ligands

From: Kristina Furse (kfurse_at_nd.edu)
Date: Thu Oct 26 2006 - 16:41:49 CDT

David-

Be a little careful if you choose an existing atom type to use for your ND1
atom--make sure there aren't existing parameters for that atom type that are
inappropriate for your HIS. One safe way to do it would be to define a totally
new atom type. You will have to supply all of the bond, angle, etc. paramters
for your new type in the frcmod, but you can just copy the ones you want to
preseve from parm99 (or whatever forcefield you are using) and change the atom
type of the N to whatever you name your new type, then customize the parameters
you want to change.

Good luck!
Kristina

Quoting David LeBard <david.lebard_at_asu.edu>:

> Hi All,
>
> I would like to simulate a system with two HIS ligands that are bound to
> a metal atom. Each ligand has slightly different parameters for
> equilibrium bond distances to the metal, angle terms between the metal
> and HIS atoms, etc. However, I do not exactly know how to change my
> frcmod file to account for these two ligands individually.
>
> I have tried simple things like changing the ND1 atom to another type
> (ie. from NB to N*), but then I need to introduce back the missing bond
> and angle parameters for all atoms touching my new N* atom. What I
> would like to do is keep most of the intra-molecular parameters for the
> modified HIS residue, but still change the type of the ND1 atom so I can
> refer to each ND1 atom explicitly in the frcmod file. What should I be
> doing differently?
>
> I believe Ross Walker's tutorial 4 is similar to this situation, however
> the frcmod file he gives in the example has the same bond and angle
> parameters for the two slightly different HIS ligands.
>
> Thanks in advance,
> David
>
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--
Kristina Furse
Postdoctoral Research Associate
262 Stepan Chemistry Hall
Notre Dame, IN 46556
(574)631-3904

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