altering residues in .pdb files

From: Thomas Kahn (tkahn_at_usc.edu)
Date: Fri Mar 26 2010 - 18:34:53 CDT

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I need to alter some residues by deleting atoms to convert a non-standard nucleotide (which I do not have topology information for) into a standard nucleotide. The effects of such a change are not important for my experiment. I have tried to delete the necessary lines from the pdb and then use excel to renumber the atom number column so that all atom numbers maintain their original order and are consecutive, however after making these edits, VMD can not load the file. I'd appreciate any help with this problem.

Thanks,
Thomas Kahn

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