AMBER Archive (2008)

Subject: RE: AMBER: can amber read .xyz files?

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu May 08 2008 - 12:23:16 CDT

Hi Wang,

> Can amber read .xyz files? Or I have to convert it to .pdb or .crd
> and .prm formatted files?

Unfortunately not. Your best option is probably to try converting it to a
pdb or mol2 file. You can then run this through antechamber (assuming this
is for a small ligand and not a complete protein) to get you the files
required to produce a prmtop and inpcrd file for use in sander.

See section 4 of the amber tools v1.0 manual and the following tutorial for
an example of how to use antechamber:

http://www.ambermd.org/tutorials/basic/tutorial4/index.htm

Good luck,
Ross

/\
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|\oss Walker

| Assistant Research Professor |
| 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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