AMBER Archive (2005)

Subject: Re: AMBER: TI - frcmod file

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue Jul 12 2005 - 17:06:53 CDT

Dear Oliver,

I have checked out the ff03 parameters. The parameters for your system are
defined in frcmod.ff03 and parm99.dat. Here are the parameters:
- parm99.dat -
CT-CT-C -N 1 0.100 0.0 -4. phi,psi,parm94
CT-CT-C -N 1 0.07 0.0 2. phi,psi,parm94
---------------
- frcmod.ff03 -
CT-CT-C -N 1 0.0560 0.00 -3.
CT-CT-C -N 1 0.0657 180.00 -2.
CT-CT-C -N 1 0.7784 180.00 1.

H0-CT-C -N 1 0.0110 0.00 -2.
H0-CT-C -N 1 1.0607 180.00 1.
---------------
First the parm99.dat is loaded and then the frcmod.ff03 is loaded. As far
as I see, there are 5 torsional parameter defined for CT-CT-C -N. That
means that if you do a perturbation from CT-CT-C -N --> H0-CT-C -N, you
need to defined 5 torsional parameter for H0-CT-C -N, too. (If I am wrong,
please someone correct me) The way I understood this particular error is,
AMBER is doing the perturbation from one torsional parameter to another
torsional parameters. As a result, we should define the same number of
torsional parameters for both states. So, I would have put the following
extra parameters in my frcmod.mod file:

H0-CT-C -N 1 0.0 0.00 -4.
H0-CT-C -N 1 0.0 0.00 -3.
H0-CT-C -N 1 0.0 0.00 2.

I would like to know what others think about this.

Best,

On Tue, 12 Jul 2005, Oliver Hucke wrote:

> Dear All,
>
> I am setting up a TI simulation of the change of an ALA in a ligand
> binding site of a protein to a GLY. The attached jpeg file shows the
> changes of atom types I apply. In the process of preparing the frcmod
> file for the atom type changes many errors of the following type
> appeared when I tried to use my frcmod file with leap:
>
> --- from leap output ---
> *** Proper torsion parameters missing ***
> atom names: CB-CA-C-N
> atom types: CT-CT-C-N =pert=> H0-CT-C-N
> Please add a dummy parameter of multiplicity 1
> for the pert types to your parameter set.
> - e.g. H0-CT-C-N 1 0.0 0. 1.
> (This is because multiple torsional potentials may apply to a
> single torsion, and each is perturbed individually in gibbs.)
> --- end of excerpt from leap output ---
>
> After doing what leap recommended, i.e. after adding all recommended
> dummy torsions to my frcmod file, everything seems to be fine, i.e. I am
> able to write the prmtop and crd output files with leap. (My frcmod file
> that can be used with leap without problems is also attached).
> BUT: some of the dummie torsions I had to add were actually "real"
> torsions defined in the force field that I am using (ff03).
> For example, leap asked me to add the following dummy torsion:
>
> H0-CT-C-N 1 0.0 0. 1.
>
> But in frcmod.03 I find:
> H0-CT-C -N 1 0.0110 0.00 -2.
> H0-CT-C -N 1 1.0607 180.00 1.
>
> Does using the dummy torsion in my frcmod file for the perturbation not
> change these parameters defined in frcmod.ff03?
>
> Thank you very much,
> Oliver
>
> 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu