where is your amber folder?
The message "Permission denied" means you need to run as root, which is NOT
recommended to do so.
Can you just either
- use a tar file of amber?
- copy previous-installed amber to some where else in your $HOME folder?
Hai
On Tue, Jan 17, 2017 at 10:08 PM, Coleman, Marcus [JRDUS Non-J&J] <
mcolem19.its.jnj.com> wrote:
> Thanks!
>
> I ran : "Make distclean" (started over)
>
> Change to regular user and ran: "./configure -cuda gnu"
>
> I am getting below error. Any suggestion would be greatly appreciated!
>
> [mcolem19.f2 amber16]$ ./configure -cuda gnu
> Checking for updates...
> Checking for available patches online. This may take a few seconds...
>
> Available AmberTools 16 patches:
>
> No patches available
>
> Available Amber 16 patches:
>
> No patches available
>
> require development version of PythonCompatible Python found! Using
> CUDA Version 8.0 detected
> Configuring for SM2.0, SM3.0, SM5.0, SM5.2, SM5.3, SM6.0 and SM6.1
>
> Obtaining the gnu compiler suite versions, e.g.:
> gcc -v
> The C version is 4.8.5
> The Fortran version is 4.8.5
> ./configure2: line 2254: testp.c: Permission denied
>
> Testing the gcc compiler:
> gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp
> testp.c
> gcc: error: testp.c: No such file or directory
> gcc: fatal error: no input files
> compilation terminated.
> ./configure2: line 2266: ./testp: No such file or directory
> Error: Unable to compile a C program using gcc -fPIC
> -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> Please check your compiler settings or configure flags.
> Configure failed due to the errors above!
> [mcolem19.f2 amber16]$
>
> ####
>
> [mcolem19.f2 amber16]$ whereis gcc
> gcc: /usr/bin/gcc /usr/lib/gcc /usr/libexec/gcc
> /usr/share/man/man1/gcc.1.gz
>
> [mcolem19.f2 amber16]$ gcc --version
> gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-11)
> Copyright (C) 2015 Free Software Foundation, Inc.
> This is free software; see the source for copying conditions. There is NO
> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
>
> [mcolem19.f2 amber16]$ which gcc
> /usr/bin/gcc
> [mcolem19.f2 amber16]$
>
>
>
> -----Original Message-----
> From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
> Sent: Tuesday, January 17, 2017 4:24 PM
> To: AMBER Mailing List
> Subject: [EXTERNAL] 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Jan 17 2017 - 19:30:04 PST
