AMBER Archive (2002)

Subject: RE: Water molecule numbering

From: Shixiang Yan (sy8_at_SCIRES.ACF.NYU.EDU)
Date: Thu Jul 25 2002 - 21:28:02 CDT

yes.. furthermore, be sure to have a TER line for each water molecule you
have in your system including those crystal waters.. yan

On Thu, 25 Jul 2002, Masaki Tomimoto wrote:

> Hi,
>
> In that case, should atom number as well as residue number be continuous?
>
> Masaki Tomimoto
>
> -----Original Message-----
> From: Shixiang Yan [mailto:sy8_at_scires.acf.nyu.edu]
> Sent: Thursday, July 25, 2002 4:25 PM
> To: Masaki Tomimoto
> Cc: amber_at_heimdal.compchem.ucsf.edu
> Subject: Re: Water molecule numbering
>
>
> 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
> >
>