AMBER Archive (2005)

Subject: Re: AMBER: Dummy Atoms: How to create them?

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue Jan 04 2005 - 21:25:24 CST

Dear Case,

I have done the following procedure to create the top/crd pert file for my
molecule:

I have created a new residue, named RC1, following the Workshop tutorial,
Example 3 (I guess). This residue is just a cytosine molecule with extra 2
dummy atoms in it. The charges were derived using RED and for the atom
types, I have used the atom types of RC residue in leaprc.ff99. I saved
this new residue in cyto.lib.

When I load a .pdb structure which has RC1 residues, xleap defines them as
RC1 residues I have created. But when I try to use the following command
in xleap it gives an error.

> saveamberparm RC1 deneme.top deneme.crd
saveAmberParm: There are no parameter sets loaded

If we create a .lib file, does not that include the parameters in them?
Thanks in advance.

On Thu, 30 Dec 2004, David A. Case wrote:

> On Thu, Dec 30, 2004, Ilyas Yildirim wrote:
> >
> > Name Type Charge Element Pert.name Pert.type Delta.charge
> > O2 O -0.6252 O N2 N* (a number)
> > DH1 0.0000 ? H12 H (a number)
> > DH2 0.0000 ? H22 H (a number)
>
> You have to give atoms DH1 and DH2 at type, probably a dummy ("DU")
>
> > FATAL: Atom .R< 15>.A<DH1 1> does not have a type.
> > FATAL: Atom .R< 15>.A<DH2 2> does not have a type.
>
> This error is caused by the lack of type above.
>
> > As far as I understood, we need to first create input files for leap using
> > antechamber.
>
> You can't use antechamber with dummy atoms. You can get parameters for the
> beginning and end states, then enter them by hand into the perturbation
> calculation.
>
> ....good luck....dac
>
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
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