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---
> radius of gyration: 7.294
FAILED (OK if gyration radius is about 7 or 8)
=====================================================
Running test to compute NAB energy of 3dfr minus waters.
Compare the NAB energy with the previously computed Amber energy:
Amber8 total energy is 5184.0880
NAB total energy is 5184.0880
PASSED
=====================================================
Running test to create Amber force-field description
PASSED
=====================================================
checking the prmtop file:
PASSED
=====================================================
Running test to compute GB Newton-Raphson and normal modes:
PASSED
=====================================================
Running test to compute non-GB Newton-Raphson and normal modes:
PASSED
=====================================================
Running test to create a simple mmCIF file
PASSED
=====================================================
Running test to do simple xmin minimization
PASSED
=====================================================
Running test to compute GB normal modes using DSYEVD:
PASSED
=====================================================
Running test to compute GB normal modes using DSAUPD:
PASSED
=====================================================
Running test to compute Langevin modes:
PASSED
=====================================================
Running test to do simple lmod optimization
1c1
< Glob. min. E = -122.793 kcal/mol
---
> Glob. min. E = -122.191 kcal/mol
FAILED (probably OK if energy is -115 to -125)
=====================================================
Running test to do simple minimization
(This tests the generalized Born implementation)
PASSED
=====================================================
make[1]: Leaving directory `/home/program/amber10/test/nab'
cd ptraj_rmsa && ./Run.rms
diffing rms.dat.save with rms.dat
PASSED
==============================================================
cd ptraj_rms && ./Run.rms
ptraj: test rms and 2drms commands
diffing rms_fit.dat.save with rms_fit.dat
PASSED
==============================================================
diffing rms_nofit.dat.save with rms_nofit.dat
PASSED
==============================================================
diffing rms2d.ps.save with rms2d.ps
PASSED
==============================================================
cd ptraj_matrix && ./Run.matrix
ptraj: analyze fluctuation matrices
diffing 1rrb_vac_distmat.dat.save with 1rrb_vac_distmat.dat
PASSED
==============================================================
diffing 1rrb_vac_mwcovarmat_evecs.dat.save with
1rrb_vac_mwcovarmat_evecs.dat
PASSED
==============================================================
diffing 1rrb_vac_distcovarmat_evecs.dat.save with
1rrb_vac_distcovarmat_evecs.dat
PASSED
==============================================================
cd antechamber/top2mol2 && ./Run.top2mol2
diffing sustiva.mol2.save with sustiva.mol2
PASSED
==============================================================
diffing dna.mol2.save with dna.mol2
PASSED
==============================================================
diffing dna_wat.mol2.save with dna_wat.mol2
PASSED
==============================================================
diffing aa.mol2.save with aa.mol2
PASSED
==============================================================
cd antechamber/database && ./Run.database
diffing total.frcmod.save with total.frcmod
PASSED
==============================================================
diffing total.prepi.save with total.prepi
PASSED
==============================================================
cd antechamber/bondtype && ./Run.bondtype
diffing ABAKOE.prepi.save with ABAKOE.prepi
PASSED
==============================================================
diffing PFPHHG02.prepi.save with PFPHHG02.prepi
PASSED
==============================================================
diffing fluorescein2.mol2.save with fluorescein2.mol2
PASSED
==============================================================
diffing fluorescein_f2.mol2.save with fluorescein_f2.mol2
PASSED
==============================================================
cd antechamber/c60 && ./Run.c60
diffing buckyball.mol2.save with buckyball.mol2
PASSED
==============================================================
diffing buckyball.gzmat.save with buckyball.gzmat
PASSED
==============================================================
diffing buckyball.jcrt.save with buckyball.jcrt
PASSED
==============================================================
diffing buckyball.prepi.save with buckyball.prepi
PASSED
==============================================================
diffing buckyball.ac.save with buckyball.ac
PASSED
==============================================================
cd antechamber/charmm && ./Run.charmm
diffing ala2.inp.save with ala2.inp
PASSED
==============================================================
diffing ala2.rtf.save with ala2.rtf
PASSED
==============================================================
diffing ala2.prm.save with ala2.prm
PASSED
==============================================================
diffing ala2_charmm.mol2.save with ala2_charmm.mol2
PASSED
==============================================================
cd antechamber/chemokine && ./Run.1b2t
diffing 1b2t.mol2.save with 1b2t.mol2
PASSED
==============================================================
diffing 1b2t.ac.save with 1b2t.ac
PASSED
==============================================================
cd antechamber/tp && ./Run.tp
diffing tp.mol2.save with tp.mol2
PASSED
==============================================================
diffing frcmod.save with frcmod
PASSED
==============================================================
cd antechamber/ash && ./Run.ash
diffing ash.mol2.save with ash.mol2
PASSED
==============================================================
diffing frcmod.save with frcmod
PASSED
==============================================================
cd antechamber/sustiva && ./Run.sustiva
diffing sustiva.mol2.save with sustiva.mol2
PASSED
==============================================================
diffing frcmod.save with frcmod
PASSED
==============================================================
diffing leap.out.save with leap.out
PASSED
==============================================================
cd antechamber/fluorescein && ./Run.fluorescein
diffing fluorescein.mol2.save with fluorescein.mol2
PASSED
==============================================================
diffing frcmod.save with frcmod
PASSED
==============================================================
cd antechamber/guanine_amber && ./Run.guanine_amber
diffing DGN.mol2.save with DGN.mol2
PASSED
==============================================================
cd antechamber/fpph && ./Run.fpph_resp
diffing fpph_resp.mol2.save with fpph_resp.mol2
PASSED
==============================================================
cd antechamber/residuegen && ./Run.ala
diffing ala.ac.save with ala.ac
PASSED
==============================================================
diffing ala.esp.save with ala.esp
PASSED
==============================================================
diffing ala.prep.save with ala.prep
PASSED
==============================================================
(cd leap && ./Run.tleap)
AMBERHOME is set to /home/program/amber10
Running leap tests on ./tleap -> ../../exe/teLeap
building force field libraries:
'91 ff..
diffing ../../dat/leap/lib/all_amino91.lib with all_amino91.lib
PASSED
==============================================================
diffing ../../dat/leap/lib/all_aminoct91.lib with all_aminoct91.lib
PASSED
==============================================================
diffing ../../dat/leap/lib/all_aminont91.lib with all_aminont91.lib
PASSED
==============================================================
diffing ../../dat/leap/lib/all_nucleic91.lib with all_nucleic91.lib
PASSED
==============================================================
diffing ../../dat/leap/lib/ions91.lib with ions91.lib
PASSED
==============================================================
'94 ff..
diffing ../../dat/leap/lib/all_amino94.lib with all_amino94.lib
PASSED
==============================================================
diffing ../../dat/leap/lib/all_aminoct94.lib with all_aminoct94.lib
PASSED
==============================================================
diffing ../../dat/leap/lib/all_aminont94.lib with all_aminont94.lib
PASSED
==============================================================
diffing ../../dat/leap/lib/all_nucleic94.lib with all_nucleic94.lib
PASSED
==============================================================
diffing ../../dat/leap/lib/ions94.lib with ions94.lib
PASSED
==============================================================
loadpdb and saveamberparm: 94 ff..
- aminoan94
comparing topology to earlier leap version..
diffing ff94/all_aminoan94.top with all_aminoan94.top
PASSED
==============================================================
comparing sander energies
diffing ff94/sander_mdout.aminoan94.save with ff94/sander_mdout.aminoan94
PASSED
==============================================================
- aminonc94
comparing topology to earlier leap version..
diffing ff94/all_aminonc94.top with all_aminonc94.top
PASSED
==============================================================
comparing sander energies
diffing ff94/sander_mdout.aminonc94.save with ff94/sander_mdout.aminonc94
PASSED
==============================================================
- dna94
comparing topology to earlier leap version..
diffing ff94/all_dna94.top with all_dna94.top
PASSED
==============================================================
comparing sander energies
diffing ff94/sander_mdout.dna94.save with ff94/sander_mdout.dna94
PASSED
==============================================================
- rna94
comparing topology to earlier leap version..
diffing ff94/all_rna94.top with all_rna94.top
PASSED
==============================================================
comparing sander energies
diffing ff94/sander_mdout.rna94.save with ff94/sander_mdout.rna94
PASSED
==============================================================
--------------------------------------------------------------
Notes:
- If all tests PASSED, you can 'rm *.log *.out *.lib *.top'
- For a discussion of energy differences (sander*.dif)
see 0README.
- It is common to see round-off differences in the
<bulding force field libraries> portion of these tests
--------------------------------------------------------------
(cd sleap && make test )
make[1]: Entering directory `/home/program/amber10/test/sleap'
rm -f `find . -name "*.dif"`
rm -f TEST_FAILURES.diff
cd mdlsdf; ./Run.mdlsdf
/bin/rm: remove write-protected regular file `crown_2.sdf'? diffing
crown_2.sdf.save with crown_2.sdf
PASSED
==============================================================
cd tripos; ./Run.tripos
diffing wy.mol2.save with wy.mol2
PASSED
==============================================================
cd pdbent; ./Run.pdbent
diffing 1hpv.mol2.save with 1hpv.mol2
PASSED
==============================================================
cd pdbent; ./Run.pdbent2
diffing mdl_1hpv.mol2.save with mdl_1hpv.mol2
PASSED
==============================================================
cd offlib; ./Run.off
diffing hpv.off.save with hpv.off
PASSED
==============================================================
cd source; ./Run.source
diffing source.out.save with source.out
PASSED
==============================================================
cd prmtop; ./Run.prmtop1
diffing hpv.top.save with hpv.top
PASSED
==============================================================
diffing hpv.xyz.save with hpv.xyz
PASSED
==============================================================
cd prmtop; ./Run.prmtop2
this is long test, wait patiently.....
diffing box.out.save with box.out
PASSED
==============================================================
diffing hpv_box.top.save with hpv_box.top
PASSED
==============================================================
cd prmtop; ./Run.prmtop3
this is a long test, wait patiently...
diffing hpv_cap.top.save with hpv_cap.top
PASSED
==============================================================
cd prmtop; ./Run.prmtoppol
diffing ubqpol.top.save with ubqpol.top
PASSED
==============================================================
diffing ubqpol.xyz.save with ubqpol.xyz
PASSED
==============================================================
cd solvate; ./Run.solvatebox
long test, wait patiently...
diffing hpvbox.pdb.save with hpvbox.pdb
PASSED
==============================================================
diffing hpvbox.top.save with hpvbox.top
PASSED
==============================================================
cd solvate; ./Run.solvatebox_closeness
long test, wait patiently...
diffing hpvbox_closeness.pdb.save with hpvbox_closeness.pdb
PASSED
==============================================================
cd solvate; ./Run.solvatecap
diffing hpvcap.pdb.save with hpvcap.pdb
PASSED
==============================================================
cd solvate; ./Run.solvateoct
long test, wait patiently...
diffing hpvoct.pdb.save with hpvoct.pdb
PASSED
==============================================================
cd solvate; ./Run.solvateshell
long test, wait patiently...
diffing hpvshell.pdb.save with hpvshell.pdb
PASSED
==============================================================
cd amoeba; ./Run.amoeba
diffing jac_2.prmtop.save with jac_2.prmtop
PASSED
==============================================================
cd amoeba; ./Run.amoeba_sol
diffing hpv.prmtop.save with hpv.prmtop
PASSED
==============================================================
cd builder; ./Run.builder
diffing water.mol2.save with water.mol2
PASSED
==============================================================
diffing wat2.mol2.save with wat2.mol2
PASSED
==============================================================
cd addions; ./Run.addions
diffing hpv_ion.pdb.save with hpv_ion.pdb
PASSED
==============================================================
cd molinfo; ./Run.molinfo
diffing leap.out.save with leap.out
PASSED
==============================================================
cd polymer; ./Run.polymer
rm: remove write-protected regular file `combine.mol2'? rm: remove
write-protected regular file `sequence.mol2'? diffing combine.mol2.save with
combine.mol2
PASSED
==============================================================
diffing sequence.mol2.save with sequence.mol2
PASSED
==============================================================
cd polymer; ./Run.impose
rm: remove write-protected regular file `impose.out'?
rm: remove write-protected regular file `impose.mol2'?
./Run.impose: line 83: impose.out: Permission denied
diffing impose.out.save with impose.out
PASSED
==============================================================
diffing impose.mol2.save with impose.mol2
PASSED
==============================================================
cd polymer; ./Run.polymer2
rm: remove write-protected regular file `aa.mol2'?
diffing aa.mol2.save with aa.mol2
PASSED
==============================================================
cd polymer; ./Run.zmatrix
rm: remove write-protected regular file `zmatrix.out'?
rm: remove write-protected regular file `meoh.mol2'?
./Run.zmatrix: line 64: zmatrix.out: Permission denied
diffing zmatrix.out.save with zmatrix.out
PASSED
==============================================================
diffing meoh.mol2.save with meoh.mol2
PASSED
==============================================================
cd bondbydis; ./Run.bondbydis
rm: remove write-protected regular file `wy.sdf'?
diffing wy.sdf.save with wy.sdf
PASSED
==============================================================
cd DNA; ./Run.DNA1
diffing 132d.mol2.save with 132d.mol2
PASSED
==============================================================
cd DNA; ./Run.DNA2
diffing 32d.top.save with 32d.top
PASSED
==============================================================
cd oldleap; ./Run.oldleap
diffing ff91/all_amino91.lib.save with ff91/all_amino91.lib
PASSED
==============================================================
diffing ff91/all_aminont91.lib.save with ff91/all_aminont91.lib
PASSED
==============================================================
diffing ff91/all_aminoct91.lib.save with ff91/all_aminoct91.lib
PASSED
==============================================================
diffing ff91/all_nucleic91.lib.save with ff91/all_nucleic91.lib
PASSED
==============================================================
diffing ff94/all_amino94.lib.save with ff94/all_amino94.lib
PASSED
==============================================================
diffing ff94/all_aminont94.lib.save with ff94/all_aminont94.lib
PASSED
==============================================================
diffing ff94/all_aminoct94.lib.save with ff94/all_aminoct94.lib
PASSED
==============================================================
diffing ff94/all_nucleic94.lib.save with ff94/all_nucleic94.lib
PASSED
==============================================================
diffing ff94/all_aminoan94.top.save with ff94/all_aminoan94.top
PASSED
==============================================================
diffing ff94/all_aminoan94.crd.save with ff94/all_aminoan94.crd
PASSED
==============================================================
diffing ff94/all_aminonc94.top.save with ff94/all_aminonc94.top
PASSED
==============================================================
diffing ff94/all_aminonc94.crd.save with ff94/all_aminonc94.crd
PASSED
==============================================================
diffing ff94/all_dna94.top.save with ff94/all_dna94.top
PASSED
==============================================================
diffing ff94/all_dna94.crd.save with ff94/all_dna94.crd
PASSED
==============================================================
diffing ff94/all_rna94.top.save with ff94/all_rna94.top
PASSED
==============================================================
diffing ff94/all_rna94.crd.save with ff94/all_rna94.crd
PASSED
==============================================================
cd disulfide; ./Run.auto
diffing crn.mol2.save with crn.mol2
PASSED
==============================================================
cd disulfide; ./Run.manu
diffing crn.mol2.save with crn.mol2
PASSED
==============================================================
cd disulfide; ./Run.auto.H
diffing crn.H.mol2.save with crn.H.mol2
PASSED
==============================================================
diffing crn.top.save with crn.top
PASSED
==============================================================
diffing crn.xyz.save with crn.xyz
PASSED
==============================================================
make[1]: Leaving directory `/home/program/amber10/test/sleap'
(cd resp && ./Run.ade )
RESP stage 1:
diffing ade_1st.out.save with ade_1st.out
PASSED
==============================================================
diffing ade_1st.pch.save with ade_1st.pch
PASSED
==============================================================
diffing ade_1st_calc.esp.save with ade_1st_calc.esp
PASSED
==============================================================
RESP stage 2:
diffing ade_1st.chg.save with ade_1st.chg
PASSED
==============================================================
diffing ade_2nd.out.save with ade_2nd.out
PASSED
==============================================================
diffing ade_2nd.pch.save with ade_2nd.pch
PASSED
==============================================================
diffing ade_2nd.chg.save with ade_2nd.chg
PASSED
==============================================================
(cd reduce && ./Run.reduce )
diffing 1ubqH.pdb.save with 1ubqH.pdb
PASSED
==============================================================
Finished test suite for AmberTools
2010/11/9 Ray Luo, Ph.D. <ray.luo.uci.edu>
> Are you able to reproduce the mmpbsa examples? If not, make sure your
> installation is clean by removing the previous installation and reinstall.
>
> All the best,
> Ray
>
> On Mon, Nov 8, 2010 at 6:26 AM, Alice Wang <compu.chem.w.gmail.com> wrote:
>
> > 2010/11/8 Alice Wang <compu.chem.w.gmail.com>
> >
> > > Dear,
> > >
> > > I had use amber10 (ambertool1.2) to calculate the mmpbsa.
> > >
> > > In cal. the binding energy, the error is
> > >
> > >
> > > Use of uninitialized value in concatenation (.) or string at
> > > /home/program/amber10/src/mm_pbsa/mm_pbsa_calceneent.pm line 191.
> > > Can't exec "-O": No such file or directory at
> > > /home/program/amber10/src/mm_pbsa/mm_pbsa_calceneent.pm line 197.
> > > -O -i sander_com.in -o sander_com.1.out -c
> > > ../snapmd1/snapshot_com.crd.1 -p ../com.top not successful
> > >
> > > [1]+ Exit 2 mm_pbsa.pl mm_pbsa.in
> > >
> > > I had read the just patch the amber10 and ambertool1.2 patches.
> > >
> > > Before, mm_pbsa cal. is right.......
> > > I had install ambertool1.4, but find my system is too old. I come back
> to
> > > amber10/ambertool1.2, and patched the fixes, then get this errors
> > >
> > > any advices, thanks very much!
> > >
> > > Alice Wang
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Nov 08 2010 - 16:00:02 PST