This post explains for how to  manually assign a dedicated IP address to a subdomain by command line,

Assume that, the below details are subdomain username and Dedicated IP,

Sub-Domain: linuxfaq.domain.com (linuxfaq)
User Name : domain
IP Address: 1.2.3.4

Step 1: Assign IP Address

Once logged into your server via SSH with root privilege open to the /var/cpanel/userdata directory.

# cd /var/cpanel/userdata/domain/

open the subdomain file by any text editor vi, vim, nano, remove the existing IP and add to dedicated IP address, ip: 1.2.3.4
 
# vi linuxfaq.domain.com


documentroot: /home/domain/public_html/linuxfaq

group: domain

hascgi: 0

homedir: /home/domain

ip: 1.2.3.4

ipv6: ~

no_cache_update: 0

owner: root

phpopenbasedirprotect: 1

serveradmin: webmaster@linuxfaq.domain.com

serveralias: www.linuxfaq.domain.com

servername: linuxfaq.domain.com

usecanonicalname: 'Off'

user: domain

userdirprotect: ''

step 2: Rebuild and restart Apache

After changes the file rebuild and restart Apache,
 
# /scripts/rebuildhttpdconf


info [rebuildhttpdconf] Missing owner for domain host3.domain.com, force lookup to root

Built /usr/local/apache/conf/httpd.conf OK

Step 3: Reserve IP Address for subdomain:

Open the domainips name
 
# vim /etc/domainips


#domainips v1

1.2.3.4: linuxfaq.domain.com

step4: Rebuild IP Pool

To execute below script assign free ip's
 
#/scripts/rebuildippool
The system has 1 free IP.


step5: DNS configuration  

Open a main domain named db file and Set the A record,
 
# vim /var/named/domain.com.db


linuxfaq    3600     IN    A    1.2.3.4

www.linuxfaq    3600    IN    A    1.2.3.4

Verify the named zone,
 
# /usr/sbin/named-checkzone domain.com /var/named/domain.com.db


zone domain.com/IN: loaded serial 2014100302

OK

Restart named service
 
# /etc/init.d/named restart


Stopping named: .                                          [  OK  ]

Starting named:                                            [  OK  ]

To check whether the named is working fine,
 
# ps aux | grep named


named     732080 17.6  0.8 402720 33852 ?        Ssl  15:15   0:01 /usr/sbin/named -u named

root      732125  0.0  0.0   6384   700 pts/2    S+   15:16   0:00 grep named

Also check the name server, and A record,
 
#  dig linuxfaq.domain.com


; <<>> DiG 9.8.2rc1-RedHat-9.8.2-0.23.rc1.el6_5.1 <<>> linuxfaq.domain.com

;; global options: +cmd

;; Got answer:

;; ->>HEADER<<- opcode: QUERY, status: NOERROR, id: 48207

;; flags: qr rd ra; QUERY: 1, ANSWER: 1, AUTHORITY: 2, ADDITIONAL: 2



;; QUESTION SECTION:

;linuxfaq.domain.com.    IN    A



;; ANSWER SECTION:

linuxfaq.domain.com. 3600    IN    A    1.2.3.4



;; AUTHORITY SECTION:

domain.com.    86400    IN    NS    ns5.domain.com.

domain.com.    86400    IN    NS    ns6.domain.com.



;; ADDITIONAL SECTION:

ns6.domain.com.    288    IN    A    192.168.0.1

ns5.domain.com.    288    IN    A    192.168.0.2



;; Query time: 45 msec

;; SERVER: 127.0.0.1#53(127.0.0.1)

;; WHEN: Sat Sep 27 15:16:13 2014

;; MSG SIZE  rcvd: 142