AMBER Archive (2007)

Subject: RE: AMBER: solvateCap minin and mdin for qm-mm dftb

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Fri Aug 24 2007 - 16:37:12 CDT

Yes, hurried I did wrong. The ambpdb-generated pdb (from inpcrd) shows the cap
centered where I asked and the solute well outside. Normally I take great care
at graphics.

All to be resumed on Sunday. Tomorrow chukards.

Thanks

francesco

--- Ross Walker <ross_at_rosswalker.co.uk> wrote:

> > I forgot to examine the cap of solvent in xleap. Now, how are
> > inpcrd rest mdcrd
> > files to be handled with VMD?
>
> Select the option with no box - this is something like "Amber Coordinates"
> or something like that - basically the same one you would pick for a gas
> phase simulation.
>
> As for the initial input why not use ambpdb to build a pdb from the prmtop
> and inpcrd file you generated and visualize it to check everything looks
> okay - Or even better load the prmtop and inpcrd file (specify amber restart
> as the type) in vmd and this will show you both atom positions and all the
> bonding info from the prmtop file - as opposed to bonding by distance with a
> pdb. This is an important step that people should "ALWAYS" do before going
> off to burn computer time.
>
> > the solute is completely out of the spherical assembly of TIP3PBOX. On
> > resizing, the solute is not resized.
>
> You probably built the spherical cap to be a long way from the solute...
>
> > To make the cap I used
> >
> > solvateCap EQE TIP3PBOX {1.2 59.9 130.3} 20.0
> >
> > where the cartesian coordinates for a central carbon atom in
> > the solute were
> > taken from the prepin file from antechamber.
>
> The prepin file contains "internal" coordinates, NOT cartesian coordinates.
> So in this case you have 1,2 which is the distance from another atom. 59.9
> which is the angle formed with two other atoms and 130.3 degrees which is a
> dihedral between the atom and 3 other atoms. Hence why your solvent cap is
> in completely the wrong place. Simplest solution would be to save a pdb file
> from leap before you add the solvent cap and then take a look at the
> coordinates in there - or alternatively since you just want the central
> carbon why not just give it the identity of the central carbon instead of
> explicit coordinates?
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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