> We *strongly* recommend you do not install as root.
Is the usual generic warning about running as root or are there specific
concerns that could arise for AMBER if it is installed and run as root?
Jim
James Kress Ph.D., President
The KressWorksR Institute
An IRS Approved 501 (c)(3) Charitable, Nonprofit Corporation
"ENGINEERING THE CURE" C
(248) 573-5499
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-----Original Message-----
From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
Sent: Tuesday, January 17, 2017 7:24 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] amber16 Centos 7
We *strongly* recommend you do not install as root. It shouldn't be
necessary and can potentially open the door to lots of problems.
As Hai suggested reading the Amber 16 manual section on Installation may be
quite helpful. Another great resource is Jason Swail's wiki
http://jswails.wikidot.com/#toc6.
-Dan
On Tue, Jan 17, 2017 at 6:50 PM, Coleman, Marcus [JRDUS Non-J&J]
<mcolem19.its.jnj.com> wrote:
> From: Coleman, Marcus [JRDUS Non-J&J]
> Sent: Tuesday, January 17, 2017 3:47 PM
> To: 'amber.ambermd.org'
> Subject: Amber16 install Centos 7 missing amber 16 tools
>
> Hello
>
>
> I have install Amber 16 on Centos 7
>
> [root.f2 ~]# cat /etc/redhat-release
> CentOS Linux release 7.3.1611 (Core)
> [root.f2 ~]# uname -r
> 3.10.0-514.2.2.el7.x86_64
> [root.f2 ~]#
>
>
> [root.f2 amber16]# ./update_amber --update Preparing to apply
> updates... please wait.
> No new updates available for AmberTools 16 No new updates available
> for Amber 16
>
> Amber16 was previously install on an identical machine but not by me.
>
> The issue is /opt/amber16/bin directory is missings tons of files compared
to the other identical machine.
> (see below)
> root.f2 ~]# cd /opt/amber16/bin
> [root.f2 bin]# pwd
> /opt/amber16/bin
> [root.f2 bin]# ls
> ######
> nc-config nccopy ncdump ncgen ncgen3 nf-config pmemd.cuda
> pmemd.cuda_DPFP pmemd.cuda_SPFP pmemd.cuda_SPXP ######
> [root.f2 bin]#
>
>
> [root.f1 ~]# cd /opt/amber16/bin
> [root.f1 bin]# pwd
> /opt/amber16/bin
> [root.f1 bin]# ls
>
> #####
> acdoctor fftw-wisdom-to-conf mmpbsa_py_energy
PdbSearcher.py sgldinfo.sh
> addles fix_new_inpcrd_vel mmpbsa_py_nabnmode pmemd
sgldwt.sh
> add_pdb frcmod2xml mm_pbsa_statistics.pl
pmemd.cuda softcore_setup.py
> AddToBox func molsurf
pmemd.cuda_DPFP sqm
> am1bcc gbnsr6 MTKppConstants
pmemd.cuda_SPFP stats
> ambmask hcp_getpdb nab
pmemd.cuda_SPXP stdLib2Sdf
> ambpdb hybrid nab2c prep2xml
superimposer
> antechamber IPMach.py nc-config prepgen
sviol
> ante-MMPBSA.py lmanal nccopy
process_mdout.perl sviol2
> atomtype makeANG_RST ncdump
process_minout.perl teLeap
> bondtype makeCHIR_RST ncgen PropPDB
tinker_to_amber
> capActiveSite makeDIST_RST ncgen3
protonator tleap
> CartHess2FC.py match nef_to_RST pymdpbsa
transform
> charmmgen match_atomname new2oldparm pytleap
translate
> charmmlipid2amber.py matextract new_crd_to_dyn reduce
tss_init
> ChBox matgen new_to_old_crd
residuegen tss_main
> CheckMD matmerge nf-config resp
tss_next
> cphstats matmul nfe-umbrella-slice respgen
ucpp
> cpinutil.py MCPB nmode rism1d
UnitCell
> cpptraj MCPB.py OptC4.py
rism3d.orave volslice
> database mdgx paramfit
rism3d.snglpnt xaLeap
> elsize mdnab parmcal
rism3d.thermo xleap
> espgen mdout2pymbar.pl parmchk sander
xparmed
> espgen.py mdout_analyzer.py parmchk2
sander.LES yacc
> fantasian minab parmed saxs_md
> FEW.pl mmE pbsa
saxs_rism
> ffgbsa mm_pbsa.pl pdb4amber senergy
> fftw-wisdom MMPBSA.py pdbSearcher
sequenceAligner
> #####
> [root.f1 bin]#
>
>
> How can I get all of the files listed above in /opt/amber16/
bin/...thanks..
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Wed Jan 18 2017 - 08:30:02 PST
