From: Axel Kohlmeyer (
Date: Tue Mar 06 2007 - 01:30:16 CST

On Mon, 5 Mar 2007, Esther Brugger wrote:

EB> Dear All,

dear esther,

EB> I met a weird problem when I read a pdb file using VMD. This pdb
EB> file was saved by VMD through AMBER trajectory file. It is no
EB> problem to read it by VMD first. Then I changed some atom names and
EB> residue names to the standard amino acid. If I tpye all these
EB> modification, it can be read by VMD correctly. Since I have thousand
EB> atoms need to be modifed, I just use the copy/paste to do it. But if
EB> I use Copy/Paste command in Nedit editor, VMD couldn't recognize the
EB> PDB file. I really don't know why. Is there someone has this

the pdb format is pretty strict in terms of column alignment.

the safest way to rename groups of atoms with the same properties
is to use atom selections within vmd to do it and then have vmd
write out the modified .pdb file.

example. to rename all water residues from HOH to WAT you can do:

set sel [atomselect top {resname HOH}]
$sel set resname WAT
$sel delete
unset sel

with automated text replacement, you have to be careful not to
replace too much text or in a way that violates the format.

the additional advantage of doing this is, that you can test
the correctness of your selection string visually e.g. by having
all atoms visualized with a lines representation and then adding
a licorice rep with only your selection.


EB> experience before? Because the atoms is a lot, I cann't type one by
EB> one. Could somebody give me some suggestions for that? Thank you
EB> very much for your help!

EB> Esther B.
EB> ---------------------------------
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Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.