VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Oct 21 2008 - 07:21:42 CDT

Try using the catdcd utility
(http://www.ks.uiuc.edu/Development/MDTools/catdcd/), which lets you
dump coordinates from a dcd to a wide variety of formats (you could, for
example, write to a pdb if you must have ascii coordinates).
Best,
Peter

JONATHAN BLACK wrote:
> hi guys. i am a biologist and i haven't been programming in perl for a long time so my question may seem a little naive but i'm at a total loss and any help would be appreciated. i need a perl script to convert some binary files (.dcd if anyone knows what they are) to ascii or just extract the ascii that they contain. i tried plain read with no results. i searched the net and i only found this code :
>
> use warnings;
> use strict;
> @ARGV == 2 or die "usage: $0 in_filename out_filename\n";
> # get first argument, i.e filename my $in_filename = shift;
> print "You chose input \n";
> my $out_filename = shift;
> print "You chose output \n";
> #set infile to binary mode open INFILE, '', $out_filename or die "can't open $out_filename: $!";
> # read 8 bytes at a time
> $/ = \8;
> while ( )
> {
> print OUTFILE join( ', ', map sprintf( '0x%04x', $_ ), unpack 'S*', $_ + ), "\n";
> }
>
> but when i run it it comes out with four columns of something seeming like hexadecimal (0xe15d ...). The dcd files are about 700 mb so i can't upload it for you to see it, but i managed to cut the first 80kb of it with hexedit and i upload it here: http://www.gigasize.com/get.php?d=7qfs5f331bf Does anyone have any idea or some plain guidelines because i really need get it done for my work. Thanks anyway!
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