AMBER Archive (2005)

Subject: Re: AMBER: Protein ions?

From: Anthony Cruz (acb15885_at_uprm.edu)
Date: Thu Jun 02 2005 - 11:45:34 CDT

Thank you Stefano this resolve my problem!

On Thursday 02 June 2005 10:57 am, Stefano Federico Massimiliano Pieraccini
(Stefano.Pieraccini) wrote:
> Dear Anthony,
>
> Sodium and calcium are included in parm99, so you have the parameters,
> but a prep file for calcium is not included in the .in files, so you
> have to create your own and load it in leap with the
> command "loadamberprep file_name.prep". A prep file with a single ion
> is very simple and should look like this one we used to solve a
> similar problem
>
> 0 0 2
>
> Calcium Ion
> CAL.res
> CAL INT 0
> CORR OMIT DU BEG
> 0.000000
> 1 DUMM DU M 0 -1 -2 0.0000 0.0000 0.0000 0.000
> 2 DUMM DU M 1 0 -1 1.0000 0.0000 0.0000 0.000
> 3 DUMM DU M 2 1 0 1.0000 90.0000 0.0000 0.000
> 4 Ca+ C0 M 3 2 1 1.0000 90.0000 180.0000 2.000
>
> DONE
> STOP
>
> The first three atoms are dummy atoms, and then there is rhe calcium
> ion with its atom type (taken from parm99), the internal coordinates
> with respect to the dummy atoms and the charge (2.000). Ca+ was the
> atom name of calcium in our PDB file, you can change it either in your
> pdb or in the prep file, but they must be the same. CAL is the residue
> name (CAL residue is formed only by atom Ca+ ), and this name must be
> the same in your PDB and prep file. The identity of names is needed to
> allow leap to recognize who is who in the different files.
>
> Best Regards
>
> Stefano Pieraccini
>
> ----- Original Message -----
> From: Anthony Cruz <acb15885_at_uprm.edu>
> Date: Thursday, June 2, 2005 4:12 pm
> Subject: AMBER: Protein ions?
>
> > Hi users:
> > I try to make a simulation of a protein that have 2 calcium and 1
> > sodium. But
> > leap don't recognize this atoms. I search the parm99.dat and the
> > sodium and
> > the calcium is included. How I could change my pdb for leap to
> > recognize it?
> >
> > Kind Regards
> > Anthony Cruz
> > -------------------------------------------------------------------
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