Pretty sure you are using some Ubuntu version, so from your initial posting trying to run apple-specific commands should fail as there is no Xcode version for Ubuntu.
What is returned by executing the following command:
ls $AMBERHOME
As I can also see that you repeatedly failed to supply a sudo password, do you have read/write permissions /usr/local/ on you system? Otherwise you should probably try to install amber in a location that does not require you to be a sudoer.
You are using bash as per your latest post, the following commands will successfully install the serial version of the AmberTools19 suite on Ubuntu 18.04 LTS using bash on a clean system. Even if you’ve already installed amber tools, make a copy of your install directory and try again.
Some important points:
1) This does require you to know your “administrator” password as a “sudoer” meaning that you should be able to run sudo commands successfully. I have hon tried updating and installing packages on a system where I do not have administrative rights so if you do not know this password there are no guarantees that the following will work.
2) Everything inside brackets [] needs to be changed to something unique for your system. Hence, "/[path]/[to]/[amber]/[install]/[directory]/“ should most likely be "/usr/local/“ based on what I see in your screen dumps.
$ sudo apt-get update && sudo apt-get upgrade -y
$ sudo apt-get install -y bc csh flex gfortran g++ xorg-dev zlib1g-dev libbz2-dev patch
$ cd /[path]/[to]/[amber]/[install]/[directory]/
$ tar xvf AmberTools19.tar.bz2
$ export AMBERHOME=/[path]/[to]/[amber]/[install]/[directory]/amber18
$ cd $AMBERHOME
$ ./configure gnu
$ source /[path]/[to]/[amber]/[install]/[directory]/amber18/amber.sh
$ echo "source /[path]/[to]/[amber]/[install]/[directory]/amber18/amber.sh" >> $HOME/.bashrc
$ make install
Good luck
> On 6 Jul 2019, at 13:20, Charu Sharma (JRF) <charu.sharma.lnmiit.ac.in> wrote:
>
> ---------- Forwarded message ---------
> From: KARISHMA SHARMA <18pph003.lnmiit.ac.in>
> Date: Sat, Jul 6, 2019, 16:49
> Subject:
> To: Charu Sharma (JRF) <charu.sharma.lnmiit.ac.in>
>
>
> It giving same error sir.
> *KARISHMA SHARMA*
> *JRF (JUNIOR RESEARCH FELLOW)*
> *PhD SCHOLAR, LNMIIT*
> <Screenshot from 2019-07-06 16-48-43.png>_______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 08 2019 - 02:30:02 PDT
