I'm facing this problem before,but i think this is not an important problem because sander works correctly.
Perhaps this problem is a calculation accuracy error. Don't worry about this.
> Date: Tue, 26 Jul 2011 15:53:19 +0500
> From: alifar76.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] problem installing amber 10
>
> Hi Nyla,
> This problem is an apparent bug, according to Dr. Case. But it doesn't come
> to bite you much. See this response earlier to a post on this community:
>
> http://archive.ambermd.org/201003/0652.html
>
> Try running a simple simulation and see if you're getting the expected
> results.
>
> Regards,
> Ali
>
> On Tue, Jul 26, 2011 at 2:19 PM, Nyla Zaman <nyla.zaman.hotmail.com> wrote:
>
> >
> > thankyou amir, ali and scott. the problem has been resolved. but now when i
> > run a test for amber , it gives the following error.
> >
> > make test
> > (find . -name '*.dif' -o -name 'profile_mpi' | \
> > while read dif ;\
> > do \
> > rm -f $dif ;\
> > done ;\
> > )
> > rm -f TEST_FAILURES.diff
> > cd dmp && ./Run.dmp
> > diffing mdout.dmp.save with mdout.dmp
> > PASSED
> > ==============================================================
> > cd adenine && ./Run.adenine
> > diffing mdout.adenine.save with mdout.adenine
> > PASSED
> > ==============================================================
> > cd cytosine && ./Run.cytosine
> > diffing cytosine.out.save with cytosine.out
> > PASSED
> > ==============================================================
> > cd nonper && ./Run.nonper
> > diffing mdout.nonper.save with mdout.nonper
> > PASSED
> > ==============================================================
> > cd nonper && ./Run.nonper.belly
> > diffing mdout.belly.save with mdout.belly
> > PASSED
> > ==============================================================
> > cd nonper && ./Run.nonper.belly.mask
> > diffing mdout.belly.mask.save with mdout.belly.mask
> > PASSED
> > ==============================================================
> > cd nonper && ./Run.nonper.min
> > diffing mdout.min.save with mdout.min
> > PASSED
> > ==============================================================
> > cd nonper && ./Run.cap
> > diffing mdout.cap.save with mdout.cap
> > PASSED
> > ==============================================================
> > cd nonper && ./Run.nonper.nocut
> > diffing mdout.nocut.save with mdout.nocut
> > PASSED
> > ==============================================================
> > cd tip4p && ./Run.tip4p
> > diffing mdout.tip4p.save with mdout.tip4p
> > PASSED
> > ==============================================================
> > cd tip4p && ./Run.tip4p_nve
> > diffing mdout.tip4p_nve.save with mdout.tip4p_nve
> > PASSED
> > ==============================================================
> > cd tip5p && ./Run.tip5p
> > diffing mdout.tip5p.save with mdout.tip5p
> > PASSED
> > ==============================================================
> > cd tip5p && ./Run.tip5p_nve
> > diffing mdout.tip5p_nve.save with mdout.tip5p_nve
> > PASSED
> > ==============================================================
> > cd 4096wat && ./Run.pure_wat
> > diffing mdout.pure_wat.save with mdout.pure_wat
> > PASSED
> > ==============================================================
> > cd 4096wat && ./Run.pure_wat_nmr_temp_reg
> > diffing mdout.pure_wat_nmr_temp.save with mdout.pure_wat_nmr_temp
> > PASSED
> > ==============================================================
> > cd 4096wat && ./Run.vrand
> > diffing mdout.vrand.save with mdout.vrand
> > PASSED
> > ==============================================================
> > cd dhfr && ./Run.dhfr
> > diffing mdout.dhfr.save with mdout.dhfr
> > PASSED
> > ==============================================================
> > cd dhfr && ./Run.dhfr.noshake
> > diffing mdout.dhfr.noshake.save with mdout.dhfr.noshake
> > PASSED
> > ==============================================================
> > cd dhfr && ./Run.dhfr.min
> > diffing mdout.dhfr.min.save with mdout.dhfr.min
> > PASSED
> > ==============================================================
> > cd gact_ips && ./Run.ips
> > diffing mdout.ips.save with mdout.ips
> > PASSED
> > ==============================================================
> > cd gact_ips && ./Run.ipsnve
> > diffing mdout.ipsnve.save with mdout.ipsnve
> > PASSED
> > ==============================================================
> > cd gact_ips && ./Run.ips_sgld
> > diffing mdout.ips_sgld.save with mdout.ips_sgld
> > PASSED
> > ==============================================================
> > cd polarizable_water && ./Run.pol_wat
> > diffing mdout.polwat.save with mdout.polwat
> > PASSED
> > ==============================================================
> > cd ubiquitin && ./Run.ubiquitin
> > diffing mdout.ubiquitin.save with mdout.ubiquitin
> > PASSED
> > ==============================================================
> > diffing mden.save with mden
> > PASSED
> > ==============================================================
> > diffing mdcrd.save with mdcrd
> > PASSED
> > ==============================================================
> > diffing mdvel.save with mdvel
> > PASSED
> > ==============================================================
> > cd dna_pol && ./Run.dna_pol
> > diffing mdout.dna_pol.save with mdout.dna_pol
> > PASSED
> > ==============================================================
> > cd trx && ./Run.trx
> > diffing mdout.trx.save with mdout.trx
> > PASSED
> > ==============================================================
> > cd trx && ./Run.trx.cpln
> > diffing mdout.trx.cpln.save with mdout.trx.cpln
> > PASSED
> > ==============================================================
> > cd rdc && ./Run.dip
> > ./Run.dip: Program error
> > make: *** [test.sander.BASIC] Error 1
> >
> >
> > > Date: Tue, 26 Jul 2011 13:43:28 +0500
> > > From: alifar76.gmail.com
> > > To: amber.ambermd.org
> > > Subject: Re: [AMBER] problem installing amber 10
> > >
> > > Hi Nyla,
> > >
> > > I was facing similar problems. As Scott has rightly said, use gfortran
> > > instead of g95. It should do the trick.
> > >
> > > # ./configure_amber –static gfortran <enter>
> > >
> > > It will generate Amber configuration file (config_amber.h)
> > >
> > > Hope it helps!
> > >
> > > Regards,
> > > Ali A. Faruqi
> > > Karachi
> > >
> > > On Tue, Jul 26, 2011 at 10:33 AM, Nyla Zaman <nyla.zaman.hotmail.com>
> > wrote:
> > >
> > > >
> > > > command:
> > > > ./configure_amber -static g95
> > > >
> > > > error:
> > > > Setting AMBERHOME to /root/nyla_working/amber10
> > > >
> > > > Setting up Amber configuration file for architecture: g95
> > > > Using parallel communications library: none
> > > > The MKL_HOME environment variable is not defined.
> > > >
> > > > Testing the C compiler:
> > > > gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -m32 -o testp
> > > > testp.c
> > > > OK
> > > >
> > > > Testing the Fortran compiler:
> > > > g95 -O0 -fno-second-underscore -o testp testp.f
> > > > ./configure_amber: line 1168: g95: command not found
> > > > ./configure_amber: line 1169: ./testp: No such file or directory
> > > > Unable to compile a Fortran program using g95 -O0
> > -fno-second-underscore
> > > > Please check your compiler settings or configure flags.
> > > >
> > > > i tried to install g95 after that and the compiler says:
> > > >
> > > > ERROR:
> > > >
> > > > ./configure_amber -static g95
> > > > Setting AMBERHOME to /root/nyla_working/amber10
> > > >
> > > > Setting up Amber configuration file for architecture: g95
> > > > Using parallel communications library: none
> > > > The MKL_HOME environment variable is not defined.
> > > >
> > > > Testing the C compiler:
> > > > gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -m32 -o testp
> > > > testp.c
> > > > OK
> > > >
> > > > Testing the Fortran compiler:
> > > > g95 -O0 -fno-second-underscore -o testp testp.f
> > > > g95: installation problem, cannot exec 'f951': No such file or
> > directory
> > > > ./configure_amber: line 1169: ./testp: No such file or directory
> > > > Unable to compile a Fortran program using g95 -O0
> > -fno-second-underscore
> > > > Please check your compiler settings or configure flags.
> > > >
> > > >
> > > >
> > > > _______________________________________________
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> > > >
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> >
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Received on Tue Jul 26 2011 - 05:00:03 PDT
