If you haven't rebooted your VM yet then the OS may not know that the disk has been expanded. So I would start with that first (or do a full VM shutdown, then startup). A second problem you'll run into is that any edits to the partition table on a drive that is in use won't be seen until the system is rebooted (or the drive otherwise made not in use). So assuming that the drive is showing up as 7GB after the reboot, you will have to enlarge the partition, then reboot again and finally issue your resize2fs command. BTW, I personally don't normally use parted, but it looks like the re-size command tries to re-size both the partition and the filesystem -- in this case, you would probably be better off just re-sizing the partition first (via fdisk), then do the filesystem after the OS is able to re-read the partition table (via a reboot). Oh, and make sure you have a good backup first.
Edit: I set up a 3GB Debian VM in VirtualBox, same as yours, and recorded a log of the steps I used to expand it to 7GB. Summary: Shut down the VM, backup the VDI file, extend the VDI, restart VM, use fdisk -- set units to sectors (u command) and display partition table (p), delete existing partitions, recreate root partition (being careful to use same starting sector as original one), recreate extended partition and swap, mark primary as bootable (a), write, reboot, then resize filesystem.
root@debian:~# cat /proc/partitions
major minor #blocks name
8 0 3145728 sda
8 1 2962432 sda1
8 2 1 sda2
8 5 180224 sda5
root@debian:~# exit
$ VBoxManage list runningvms
"Debian" {b32e56f1-a6b9-4753-a67d-19f03503f884}
$ VBoxManage controlvm Debian acpipowerbutton
$ cp Debian.vdi Debian.vdi.backup
$ VBoxManage modifyhd Debian.vdi 7168
$ VBoxManage startvm Debian
$ ssh root@192.168.56.101
root@debian:~# cat /proc/partitions
major minor #blocks name
8 0 7340032 sda
8 1 2962432 sda1
8 2 1 sda2
8 5 180224 sda5
root@debian:~# swapoff /dev/sda5
root@debian:~# fdisk /dev/sda
Command (m for help): u
Changing display/entry units to sectors
Command (m for help): p
Disk /dev/sda: 7516 MB, 7516192768 bytes
Device Boot Start End Blocks Id System
/dev/sda1 * 2048 5926911 2962432 83 Linux
Partition 1 does not end on cylinder boundary.
/dev/sda2 5928958 6289407 180225 5 Extended
Partition 2 does not end on cylinder boundary.
/dev/sda5 5928960 6289407 180224 82 Linux swap / Solaris
Command (m for help): d
Partition number (1-5): 5
Command (m for help): d
Partition number (1-5): 2
Command (m for help): d
Selected partition 1
Command (m for help): n
Command action
e extended
p primary partition (1-4)
p
Partition number (1-4): 1
First sector (63-14680063, default 63): 2048
Last sector, +sectors or +size{K,M,G} (2048-14680063, default 14680063): +6G
#Impportant! Fdisk in this case defaults to a starting sector of 63, but the original OS install started at sector 2048. You must specify the same starting sector (manually) as what was originally there.
Command (m for help): p
Disk /dev/sda: 7516 MB, 7516192768 bytes
Device Boot Start End Blocks Id System
/dev/sda1 2048 12584960 6291456+ 83 Linux
Command (m for help): n
Command action
e extended
p primary partition (1-4)
e
Partition number (1-4): 2
First sector (63-14680063, default 63): 12584961
Last sector, +sectors or +size{K,M,G} (12584961-14680063, default 14680063):
Using default value 14680063
Command (m for help): n
Command action
l logical (5 or over)
p primary partition (1-4)
l
First sector (12585024-14680063, default 12585024):
Using default value 12585024
Last sector, +sectors or +size{K,M,G} (12585024-14680063, default 14680063):
Using default value 14680063
Command (m for help): p
Device Boot Start End Blocks Id System
/dev/sda1 2048 12584960 6291456+ 83 Linux
Partition 1 does not end on cylinder boundary.
/dev/sda2 12584961 14680063 1047551+ 5 Extended
Partition 2 does not end on cylinder boundary.
/dev/sda5 12585024 14680063 1047520 83 Linux
Command (m for help): a
Partition number (1-5): 1
Command (m for help): t
Partition number (1-5): 5
Hex code (type L to list codes): 82
Changed system type of partition 5 to 82 (Linux swap / Solaris)
Command (m for help): w
The partition table has been altered!
Calling ioctl() to re-read partition table.
WARNING: Re-reading the partition table failed with error 16: Device or resource busy.
The kernel still uses the old table. The new table will be used at
the next reboot or after you run partprobe(8) or kpartx(8)
Syncing disks.
root@debian:~# reboot
$ ssh root@192.168.56.101
root@debian:~# cat /proc/partitions
major minor #blocks name
8 0 7340032 sda
8 1 6291456 sda1
8 2 1 sda2
8 5 1047520 sda5
root@debian:~# df /
Filesystem 1K-blocks Used Available Use% Mounted on
/dev/sda1 2915832 809244 1958468 30% /
root@debian:~# resize2fs /dev/sda1
resize2fs 1.41.12 (17-May-2010)
Filesystem at /dev/sda1 is mounted on /; on-line resizing required
old desc_blocks = 1, new_desc_blocks = 1
Performing an on-line resize of /dev/sda1 to 1572864 (4k) blocks.
The filesystem on /dev/sda1 is now 1572864 blocks long.
root@debian:~# df /
Filesystem 1K-blocks Used Available Use% Mounted on
/dev/sda1 6194240 810684 5071636 14% /
root@debian:~# mkswap /dev/sda5