AMBER Archive (2007)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Aug 24 2007 - 16:05:24 CDT

> 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

/\
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|\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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