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 Tue Jan 17 2017 - 16:30:04 PST
