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 - 16:00:02 PST
