AMBER Archive (2006)

Subject: Re: AMBER: Two different HIS ligands

From: David LeBard (david.lebard_at_asu.edu)
Date: Thu Oct 26 2006 - 18:16:42 CDT

Thank you Kristina! Your solution worked perfectly.

All the best,
David

On Thu, 2006-10-26 at 14:41, Kristina Furse wrote:
> 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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