AMBER Archive (2002)

Subject: Re: Water molecule numbering

From: Shixiang Yan (sy8_at_SCIRES.ACF.NYU.EDU)
Date: Thu Jul 25 2002 - 18:25:08 CDT

hi,

since the water molecules are not connected to your macromolcule, even though
they are bound waters, you can separate them from your macromolecule.
and it would be better to put them after the macromolecule.

1. prepare a pdb file of the macromolecule only, and use the right
numbering
2. load into leap to generate the .top and .crd files
3. use ambpdb to get a "clean" pdb file from those .top and .crd
4. prepare the pdb file of all the bound waters, using the consecutive
   numbers after your macromolecule. and combine them into a new pdb.
5. load into leap again, and solvate the whole thing.

hope this would help... yan

On Thu, 25 Jul 2002, Masaki Tomimoto wrote:

> Hi All,
>
> I have a question about residue numbering of water molecules. When I load a PDB file which contains bound waters onto Leap, assign parameters, save it with "saveamberparm", and then generate PDB file from CRD and TOP file with "ambpdb" command, residue numbering of water molecules are automatically changed.
>
> Have anybody found the problem before? Only me? If this is the case, is there any rule in the renumbering?
>
> Masaki Tomimoto
>