Your root.f2 machine only built gpu version while the another machine built all programs. Please check manual for further info.
Hai
> On 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..
>
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Received on Tue Jan 17 2017 - 16:30:02 PST
