RE: altering residues in .pdb files

From: Peter Jones (
Date: Fri Mar 26 2010 - 20:29:00 CDT

Hi Thomas,

sounds like you might have altered the format of the .pdb file when you used excel. Probably the best thing to do is simply delete the lines you don't want from your .pdb and then use psfgen to generate the .psf and .pdb files. Psfgen won't worry about the atom numbers or the atom order within a residue or nucleotide.

From: [] On Behalf Of Thomas Kahn []
Sent: Saturday, March 27, 2010 10:34 AM
Subject: namd-l: altering residues in .pdb files

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.

Thomas Kahn

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