From: Axel Kohlmeyer (
Date: Thu Aug 28 2008 - 15:50:21 CDT

On Thu, 28 Aug 2008, Alejandro Ortega wrote:

AO> Hello everyone,
AO> First of all, I'm e-mailing this to VMD and NAMD communities because i think
AO> this problem may affect both of them.
AO> Well, the thing is that creating a simulation requires a lot of TXT edition,
AO> at least in my personal case. I stay hours and hours editing TXT files (The
AO> *.params, *.PDB, *.PSF, etc.,) and i think that sometimes it is not
AO> necessary to do all this job. As a reference, i know how to use the
AO> "replace" command in notepad, wordpad does not have too many extra options,
AO> and excel works as well, but it is harder to use, is almost the same work
AO> than in wordpad or notepad.


it may not be so obvious, but i found it particularly useful
to use VMD scripting(!) to do lots of manipulations (renaming,
renumbering, grouping etc.) of .pdb and .psf files. it'll still
be worth learning how to use the advanced features of a good
(programming) text editor, even if only to write the scripts
to manipulate the files.

especially, repetitive replacements are much safer, when done
with a script/program. you can always see from the script what
you did and can always rerun it with little effort as soon
as you have a first working version, in case you notice a
small error.


AO> I've been thinking in creating one, it is not a great deal, it just requires
AO> basic knowledge of programming in visual basic or C++, but i am running out
AO> of time and i really need to edit high amounts of text.
AO> In brief, my question is: does someone know a program that is specialized in
AO> editing TXT files? or does someone has made a program specialized for this
AO> issue?
AO> Also, if someone knows a better way to edit large amounts of text please let
AO> me know.
AO> Thank you!
AO> Cheers,
AO> Alejandro Ortega.

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.