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
/\
\/
|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
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Received on Sun May 11 2008 - 06:07:32 PDT
