VMD-L Mailing List

From: mdcooper (mdcooper_at_uvic.ca)
Date: Fri Oct 08 2004 - 15:54:58 CDT

I am trying to build a psf file for a complex with URA, except it is a URA
molecule with an extra oxygen than the one provided in CHARMm so I have built
URA2.

I am aliasing URA to URA2 in the .pgn file.

WHen I try to run the .pgn file it gets as far as extracting the 238 residues
and then, apparently, reference bad memory and fails (ie the failure occurs
outside of VMD). This is the same thing that happens when I tried to build a
psf file with a molecule that contained hydrogens.

Can anyone help - it is driving me nutty.

thanks,

matt

ATOM 1806 CG2 ILE A 237 75.765 42.905 46.179 1.00 54.08
ATOM 1807 CD1 ILE A 237 75.871 42.087 42.450 1.00 53.68
ATOM 1808 N1 URA A 238 62.024 57.956 28.031 1.00 14.18
ATOM 1809 C2 URA A 238 61.074 57.866 29.056 1.00 15.27