I am using Kali 2017.2. I tried install a modelling software (abaqus). As the part they instructed me to follow certain command. When I run this command, and after accepting with y, all my pentesting tools got removed and no GUI from then. Any idea what it did, and how to bring my system back.

Now I have access to tty only.
Any one help me bring my system up.

you are missing out one important step:
all the output you received after entering the command (and before pressing 'y').

that is where the answer to your question lies.

but since you already did that, there's only one advice:
re-install, and in the future, read before pressing 'y' or Enter.

Welcome to LQ! LQ has recently posted the perfect answer, as a 'sticky', at the top of this Newbie Forum. (feel free to ask how to find it, if you need help finding it, and we will post the link)

It would be best to become experienced with Linux (which is the OS used in most of 'The Cloud')
before trying to be the 'expert' which the above sticky explains Kali is for.

Kali is currently offering their $30 new book FREE here: https://www.kali.org/download-kali-linux-revealed-book/

Enjoy learning; it's ok to erase & start over

p.s. Also, to demo this LQ skill, please 'Edit' #1, click the 'Go Advanced' button, then insert the word 'Kali' in this Thread Title, to help others find this info, and that free eBook!!! Thank you for your cooperation.

2 members found this post helpful.

Kali is definitely NOT a distro you want to use for every day work, unless you are a pen tester.

1 members found this post helpful.

I would take the advice of posts #3 and #4 and install a SUITABLE distro instead, if I were you.

@ondoho, why are you encouraging the use of an UN-SUITABLE distro for??

The OP does cite pentesting tools.

However installing 3D modeling software doesn't seem to make sense.

Use Kali for it's intended use, and use another distribution for desktop activities.

1 members found this post helpful.

so you think everyone who uses kali linux should be denied any help, because it would be "encouraging to use an unsuitable distro".
fine, make it your prerogative, but leave me out of it.
thank you.