Metasploit has its own version of nmap stored in /opt/metasploit/common/bin. If you want to call your the non-metasploit version of nmap, you can just call it directly using /usr/local/bin/nmap from within metasploit:
Alternatively, you can scan from outside of Metasploit and import the XML logs into Metasploit using db_import.Code:msf > /usr/local/bin/nmap -sS -T4 -O -A scanme.nmap.org[*] exec: /usr/local/bin/nmap -sS -T4 -O -A scanme.nmap.org /usr/local/bin/nmap: /opt/metasploit/common/lib/libssl.so.0.9.8: no version information available (required by /usr/local/bin/nmap) /usr/local/bin/nmap: /opt/metasploit/common/lib/libcrypto.so.0.9.8: no version information available (required by /usr/local/bin/nmap) /usr/local/bin/nmap: /opt/metasploit/common/lib/libsasl2.so.2: no version information available (required by /usr/lib/libldap_r-2.4.so.2) /usr/local/bin/nmap: /opt/metasploit/common/lib/libsasl2.so.2: no version information available (required by /usr/lib/libsvn_ra_svn-1.so.1) /usr/local/bin/nmap: /opt/metasploit/common/lib/libxml2.so.2: no version information available (required by /usr/lib/libneon-gnutls.so.27) /usr/local/bin/nmap: /opt/metasploit/common/lib/libxml2.so.2: no version information available (required by /usr/lib/libneon-gnutls.so.27) Starting Nmap 5.61TEST4 ( http://nmap.org ) at 2012-04-11 10:58 EDT Nmap scan report for scanme.nmap.org (74.207.244.221) . . .


