Re: [AMBER] Installation Problem : Amber 9

From: souvik sur <>
Date: Thu, 16 Jun 2011 11:36:36 +0530

Hello sir,

I found this after typing setenv PATH $AMBERHOME/exe:$PATH:

[souvik.masternode amber9]$ setenv PATH $AMBERHOME/exe:$PATH
-bash: setenv: command not found
[souvik.masternode amber9]$ PATH $AMBERHOME/exe:$PATH
-bash: PATH: command not found
[souvik.masternode amber9]$ $AMBERHOME/exe:$PATH
-bash: /home/souvik/Amber9/amber9/exe:/home/souvik/mpich2-1.3/bin:/usr/lib64/qt-3.3/bin:/opt/kusu/bin:/opt/kusu/sbin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/souvik/bin: No such file or directory
[souvik.masternode amber9]$ $AMBERHOME/exe
-bash: /home/souvik/Amber9/amber9/exe: is a directory
[souvik.masternode amber9]$ cd $AMBERHOME/exe
[souvik.masternode exe]$ ls
addles anal espgen make_crd_hg nmode prepgen respgen sviol2 xleap
am1bcc antechamber fantasian makeDIP_RST.dna molsurf nucgen protonate sander teLeap
amber9 atomtype crdgrow gwh makeDIP_RST.protein parmcal ptraj sander.LES tleap
ambmask bondtype database lmodprmtop makeDIST_RST new2oldparm parmchk rdparm sander.PIMD top2mol2
ambpdb divcon makeANG_RST makeSHF_RST new_crd_to_dyn pbsa README senergy translate
amoeba_parm charmmgen elsize makeCHIR_RST new_to_old_crd pol_h resp sviol xaLeap
[souvik.masternode exe]$

Souvik Sur
Ph. D. Student
Department Of Chemistry
University Of Delhi

> Date: Wed, 15 Jun 2011 09:10:46 -0400
> From:
> To:
> Subject: Re: [AMBER] Installation Problem : Amber 9
> On Wed, Jun 15, 2011, souvik sur wrote:
> >
> > I am trying to install Amber9 in Red Hat Linux Enterprise version, i
> > have done all the protocol of installation as described in CD but still
> > when I want to locate any amber command like xleap, tleap, sander etc.
> > it showed : no such file ;i have also set the AMBERHOME environment
> > and type source .cshrc, it didnot show any error and I also found
> > xleap, tleap, sander etc in amber9's exe directory, but still it is not
> > running, It showed error when I typed make serial in $AMBERHOME/exe
> > directory.
> You need to include $AMBERHOME/exe in your PATH. If you don't understand how
> to do this, see if you can find a friend who is familiar with computers to
> help you out. The internet has many Linux tutorials that might also help:
> you need to learn this sort of thing to be productive with Amber.
> You seem already to have installed the programs (since you say that you found
> them in the exe directory). So, you don't need to run "make" again, and would
> certainly not do that from the exe directory in any event.
> You need to type something like this:
> setenv PATH $AMBERHOME/exe:$PATH
> *but* you also need to do enough reading and experimenting to understand what
> is going on here.
> ...good luck...dac
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Received on Wed Jun 15 2011 - 23:30:03 PDT
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