Re: altering residues in .pdb files

Date: Mon Mar 29 2010 - 11:20:08 CDT

Hi Thomas

I hope you want to edit only PDB file. In that case this might help

1] Open your pdb file using "Word Pad" [ keep a copy of original pdb file
with you]
2] Delete unnecessary atom lines
3] Save the file [ Do not use "Save As" ]
4] Open the file using VMD
5] Save the coordinates in pdb format. [ I hope your are familiar with VMD]

Try this

> I need to alter some residues by deleting atoms to convert a
> nucleotide (which I do not have topology information for) into a
> 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
> maintain their original order and are consecutive, however after making
these edits, VMD can not load the file. I'd appreciate any help with
> problem.
> Thanks,
> Thomas Kahn

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