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Hello Andrew-- > I am attempting to run a docking simulation > similiar to the one published in JACS (2003) 125, pgs 2902-2912. In > the demonstration files, I noticed that the atom numbers in the psf > files and pdb files seem to correlate. When I use pdb2psf, the > resulting output file gives me a psf file that does not necessarily > match ATOM numbers. I have been getting errors trying to run the > simulation using other PDB files - particularly with respect to > loading the coordinates. Is this the cause, and, is there an easy cure? Atom indices themselves are not particularly important- they aren't used when reading pdb files. What's important is that each atom of each residue is present. What is the nature of the errors you are seeing? best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.9 <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkyab/AACgkQPK2zrJwS/lbYJwCfRacOyIAKZ2k0HF/hvH9S6t6C r28AnjtZicwRupKSISrcW1+oAoxxL22T =eTHi -----END PGP SIGNATURE-----
