From: Emily Moore (
Date: Thu Aug 28 2008 - 17:09:42 CDT


I completely agree with Peter. I use vim/emacs for some of my work, but for
editing text files, I use a combination of sed, awk and grep within csh or
pearl scripts. If you are comfortable in C programming, csh scripts are
simple, but they're all pretty much the same.

Good luck.

~ Emily

On 8/28/08 2:06 PM, "Peter Freddolino" <> wrote:

> Alejandro,
> there are quite a few programs out there that are dedicated text editors
> far superior to wordpad/notepad. A couple of examples from the world of
> Free software (in no particular order, so as to avoid flamewars):
> vim/gvim
> emacs
> nedit
> nano/pico
> All of these have a great deal of functionality to make editing text
> files easier and more efficient. You should be able to find one or more
> of them for whatever platform you use.
> Many of the text transformations needed for editing the files associated
> with simulation are more efficient to do on the command line using unix
> tools such as sed, awk, and grep, or scripting languages such as perl
> and python. I highly recommend becoming more familiar with at least some
> of these options.
> Best,
> Peter
> Alejandro Ortega wrote:
>> Hello everyone,
>> First of all, I'm e-mailing this to VMD and NAMD communities because i
>> think this problem may affect both of them.
>> Well, the thing is that creating a simulation requires a lot of TXT
>> edition, at least in my personal case. I stay hours and hours editing
>> TXT files (The *.params, *.PDB, *.PSF, etc.,) and i think that
>> sometimes it is not necessary to do all this job. As a reference, i
>> know how to use the "replace" command in notepad, wordpad does not
>> have too many extra options, and excel works as well, but it is harder
>> to use, is almost the same work than in wordpad or notepad.
>> I've been thinking in creating one, it is not a great deal, it just
>> requires basic knowledge of programming in visual basic or C++, but i
>> am running out of time and i really need to edit high amounts of text.
>> In brief, my question is: does someone know a program that is
>> specialized in editing TXT files? or does someone has made a program
>> specialized for this issue?
>> Also, if someone knows a better way to edit large amounts of text
>> please let me know.
>> Thank you!
>> Cheers,
>> Alejandro Ortega.