Just put in the value of the variable that you want to change to get a new setting.

For example, in the NCBI CD-Search URL given above, the database selection variable name and the three possible values can be seen in the "View source" for the HTML page:

Search Database: <select NAME="DATALIB">
<option VALUE="oasis_smart"> Smart v3.3 - 569 PSSMs
<option VALUE="oasis_pfam"> Pfam v6.6 - 3071 PSSMs
<option VALUE="oasis_sap" SELECTED> All - 3693 PSSMs
</select>
[download]

The variable name is DATALIB, with three possible values: oasis_smart, oasis_pfam, and oasis_sap. The SELECTED beside "oasis_sap" indicates that this is the default or selected value if the user does not change it.

So in your code, along with the SEQUENCE=>"$string" you also need a DATALIB=>'oasis_smart' if the Smart v3.3 database was to be the new target.

In fact, you can set all the POST parameters for the wrpsb.cgi page with code like this:

#!/usr/bin/perl

use strict;
use HTTP::Request::Common qw(POST);
use LWP::UserAgent;

my $ua = LWP::UserAgent->new;

my $string = ">CG2B_MARGL\n ";
$string .= "MLNGENVDSRIMGKVATRASSKGVKSTLGTRGALENISNVARNNLQAGAK\n";
$string .= "KELVKAKRGMTKSKATSSLQSVMGLNVEPMEKAKPQSPEPMDMSEINSAL\n";
$string .= "EAFSQNLLEGVEDIDKNDFDNPQLCSEFVNDIYQYMRKLEREFKVRTDYM\n"; 
$string .= "TIQEITERMRSILIDWLVQVHLRFHLLQETLFLTIQILDRYLEVQPVSKN\n";
$string .= "KLQLVGVTSMLIAAKYEEMYPPEIGDFVYITDNAYTKAQIRSMECNILRR\n";
$string .= "LDFSLGKPLCIHFLRRNSKAGGVDGQKHTMAKYLMELTLPEYAFVPYDPS\n"; 
$string .= "EIAAAALCLSSKILEPDMEWGTTLVHYSAYSEDHLMPIVQKMALVLKNAP\n"; 
$string .= "TAKFQAVRKKYSSAKFMNVSTISALTSSTVMDLADQMC";


my $req=POST 'http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi',
   [ SEQUENCE=>"$string", 
     DATALIB=>'oasis_sap', 
     INPUT_TYPE=>'fasta', 
     EXPECT=>'0.01',
     FILTER=>'T', 
     SMODE=>'0', 
     NHITS=>'50', 
     GRAPH=>'2', 
     PAIR=>'2', 
     GW=>'-1'];


 print "Content-type: text/html\n\n";
 print $ua->request($req)->as_string();
[download]

Running this code as, say, sample.cgi in a Web server will return a rather impressive set of match options. Or just running from the command line as, say,
perl -w sample.cgi
will give the html source code on the screen.

Hope this helps. Good luck with this enterprise.