AMBER: Tutorial one : error

From: a a <>
Date: Wed, 17 May 2006 14:01:26 +0800

Dear Ross Walker,

Thank you very much for your help, I can get the installation done, with
most of the test done. Thus, I move on to do study the tutorial. I face a
problem in tutorial one.

I follow the tutorial one, by typing a file. Then, I type the
command line:

$AMBERHOME/exe/nucgen -o -i -o nuc.out -d
$AMBERHOME/dat/leap/parm/nucgen.dat -p nuc.pdb

However, the following error message appears:

$AMBERHOME/exe/nucgen: error while loading shared libraries:
cannnot open shared object file: No such file or directory.

I checked that we got $AMBERHOME/exe/nucgen and
$AMBERHOME/dat/leap/parm/nucgen.dat in the right directories. Could you
mind to teach me what is missing here, and how to solve this problem?

Many thanks in advanced.

Best regards,

>From: "Ross Walker" <>
>To: <>
>Subject: RE: AMBER: Amber install on RedHat Linux
>Date: Thu, 4 May 2006 08:31:56 -0700
>Dear Annie,
> > These are the files in exe directory:
> > am1bcc bondtype espgen makeDIP_RST.dna
> > makeSHF_RST molsurf prepgen senergy teLeap
> > antechamber crdgrow makeANG_RST
> > makeDIP_RST.protein
> > parmcal README sviol tleap
> > atomtype database makeCHIR_RST
> > makeDIST_RST
> > parmchk respgen sviol2 xleap
> >
> > Did anything is missing?
>Yes, lots it seems you got only the things that are written in c compiled.
> > ifort -c -w95 -tpp7 -mp1 -O0 -o new2oldparm.o _new2oldparm.f
> > make[1]: ifort: Command not found
>This should be a fairly obvious error. As part of the Intel compiler
>installation it tells you (or the system admin) to modify your login
>to source the intel setup files. I.e.
>source /opt/intel/fc/9.0/bin/
>Indeed, pasting the above error message into Google gives you many useful
>Alternatively as I see below it is likely that you do not have the Intel
>compiler suite installed.
> > Since I suspect no compilation has done, I type "make -i"
>So this was a bad idea. What you told make to do is to ignore errors and
>continue, which is exactly what it did. It has gone through, ignored the
>fact that it can't find ifort as it was not setup in your path correctly
>then just merrily compiled anything written in c with the gcc compiler that
>is in your path. Hence you only got a subset of the programs compiled.
> > What should I do next? Based on the inforamtion about, do I
> > need to buy a
> > compiler, if yes, could you mind to recommend a compiler that
> > is compatible
> > with amber8 and could solve the problems I raised above?
>You need a Fortran 90 compiler to compile Amber 8 (Fortran 95 for Amber 9).
>You can download the Intel fortran compiler for Linux from the Intel site
>and it is free for personal use. Although technically for academic use one
>has to pay a licence fee to Intel. Alternatively you can use the free g95
>compiler which is available here: The attached config.h
>file ('I believe') should work for Amber 8 with g95.
>All the best
>|\oss Walker
>| HPC Consultant and Staff Scientist |
>| San Diego Supercomputer Center |
>| Tel: +1 858 822 0854 | EMail:- |
>| | PGP Key available on request |
>Note: Electronic Mail is not secure, has no guarantee of delivery, may not
>be read every day, and should not be used for urgent or sensitive issues.

><< config.h >>

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Received on Sun May 21 2006 - 06:07:04 PDT
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