We need to see the .dif files to know how serious the errors are. In a lot
of cases it will just be round off differences in the last decimal place.
These are acceptable since different machines round in different ways and
different orders of execution can lead to slightly different results. Such
round off errors are common with the antechamber test cases since this has
to do an SCF procedure on each step which results in significantly more
computational work and hence more chance for roundoff errors to propegate.
Check the .dif file for each failed test case and it should be obvious if
the errors are serious or now.
I hope this helps.
All the best
Ross
/\
\/
|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk/ | PGP Key available on request |
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be read every day, and should not be used for urgent or sensitive issues.
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Joe Nolan
> Sent: 08 February 2005 11:56
> To: amber.scripps.edu
> Subject: AMBER: Amber8 installation test possible failures
>
> Dear amber community, enclosed are the possible failures we have
> encountered when testing the installation of Amber8 on an SGI Fuel
> running IRIX 6.5, any feedback as to the severity of these errors or
> their significance would be greatly appreciated, Thank You in advance:
>
> -------------------
> 1)diffing out.p1.save with out.p1
> possible FAILURE: check out.p1.dif
> -------------------
> 2) cd pb_pgb; ./Run.pbpgb
> diffing mdout.pbpgb.save with mdout.pbpgb
> possible FAILURE: check mdout.pbpgb.dif
> -------------------
> 3)diffing ../../dat/leap/lib/all_aminoct91.lib with all_aminoct91.lib
> possible FAILURE: check all_aminoct91.lib.dif
> -------------------
> 4)diffing ../../dat/leap/lib/all_aminoct94.lib with all_aminoct94.lib
> possible FAILURE: check all_aminoct94.lib.dif
> -------------------
> 5)Running: /usr/local/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0 -o
> ANTECHAMBER_AC.AC -p gaff
>
> Total number of electrons: 58; net charge: 0
>
> Running: /usr/local/amber8/exe/divcon
>
> Running: /usr/local/amber8/exe/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o
> ANTECHAMBER_AM1BCC.AC -f ac -p
> /usr/local/amber8/dat/antechamber/BCCPARM.DAT -j 4
>
>
>
> Running: /usr/local/amber8/exe/atomtype -i ANTECHAMBER_PREP.AC0 -o
> ANTECHAMBER_PREP.AC -p gaff
>
>
> Running: /usr/local/amber8/exe/prepgen -i ANTECHAMBER_PREP.AC
> -f int -o
> tp.prepin -rn "TP " -rf molecule.res
> diffing tp.prepin.save with tp.prepin
> possible FAILURE: check tp.prepin.dif
> -------------------
> 6)diffing prmtop.save with prmtop
> possible FAILURE: check prmtop.dif
> -------------------
> 7)diffing prmtop.mol2.save with prmtop.mol2
> possible FAILURE: check prmtop.mol2.dif
> ------------------- cd antechamber/ash; ./Run.ash
> 8)Running: /usr/local/amber8/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC
> -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full
>
>
> Running: /usr/local/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0 -o
> ANTECHAMBER_AC.AC -p gaff
>
> Total number of electrons: 100; net charge: 0
>
> Running: /usr/local/amber8/exe/divcon
>
> Running: /usr/local/amber8/exe/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o
> ANTECHAMBER_AM1BCC.AC -f ac -p
> /usr/local/amber8/dat/antechamber/BCCPARM.DAT -j 4
>
>
>
> Running: /usr/local/amber8/exe/atomtype -i ANTECHAMBER_PREP.AC0 -o
> ANTECHAMBER_PREP.AC -p gaff
>
>
> Running: /usr/local/amber8/exe/prepgen -i ANTECHAMBER_PREP.AC
> -f int -o
> ash.prepin -rn "ACE " -rf molecule.res
> diffing ash.prepin.save with ash.prepin
> possible FAILURE: check ash.prepin.dif
> -------------------
> 9)diffing prmtop.save with prmtop
> possible FAILURE: check prmtop.dif
> -------------------
> 10) cd antechamber/sustiva; ./Run.sustiva
> Running: /usr/local/amber8/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC -o
> ANTECHAMBER_BOND_TYPE.AC -f ac -j full
>
>
> Running: /usr/local/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0 -o
> ANTECHAMBER_AC.AC -p gaff
>
> Total number of electrons: 160; net charge: 0
>
> Running: /usr/local/amber8/exe/divcon
>
> Running: /usr/local/amber8/exe/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o
> ANTECHAMBER_AM1BCC.AC -f ac -p
> /usr/local/amber8/dat/antechamber/BCCPARM.DAT -j 4
>
>
>
> Running: /usr/local/amber8/exe/atomtype -i ANTECHAMBER_PREP.AC0 -o
> ANTECHAMBER_PREP.AC -p gaff
>
>
> Running: /usr/local/amber8/exe/prepgen -i ANTECHAMBER_PREP.AC
> -f int -o
> sustiva.prepin -rn "SUS " -rf molecule.res
> diffing sustiva.prepin.save with sustiva.prepin
> possible FAILURE: check sustiva.prepin.dif
> --------------------
> 11)diffing prmtop.save with prmtop
> possible FAILURE: check prmtop.dif
> cd antechamber/fluorescein; ./Run.fluorescein
>
> Bond types are assigned for valence state 1 with penalty of 2
>
> Total number of electrons: 172; net charge: -2
>
> Running: /usr/local/amber8/exe/divcon
>
> Bond types are assigned for valence state 1 with penalty of 2
>
>
> diffing fluorescein.prepin.save with fluorescein.prepin
> possible FAILURE: check fluorescein.prepin.dif
> ---------------------
> 12)diffing prmtop.save with prmtop
> possible FAILURE: check prmtop.dif
> ---------------------
> 13) cd antechamber/guanine_amber; ./Run.guanine_amber
> Running: /usr/local/amber8/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC -o
> ANTECHAMBER_BOND_TYPE.AC -f ac -j full
>
>
> Running: /usr/local/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0 -o
> ANTECHAMBER_AC.AC -p amber
>
> Total number of electrons: 140; net charge: 0
>
> Running: /usr/local/amber8/exe/divcon
>
> Running: /usr/local/amber8/exe/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o
> ANTECHAMBER_AM1BCC.AC -f ac -p
> /usr/local/amber8/dat/antechamber/BCCPARM.DAT -j 4
>
>
>
> Running: /usr/local/amber8/exe/atomtype -i ANTECHAMBER_PREP.AC0 -o
> ANTECHAMBER_PREP.AC -p amber
>
>
> Running: /usr/local/amber8/exe/prepgen -i ANTECHAMBER_PREP.AC
> -f int -o
> DGN.prepin -rn "DGN " -rf molecule.res
> diffing DGN.prepin.save with DGN.prepin
> possible FAILURE: check DGN.prepin.dif
> ---------------------
> 14) cd pbsa_trx; ./Run.trxox.min
> diffing mdout.trxox.min.save with mdout.trxox.min
> possible FAILURE: check mdout.trxox.min.dif
> ---------------------
> 15) cd pbsa_dmp; ./Run.dmp.min
> diffing mdout.dmp.min.save with mdout.dmp.min
> possible FAILURE: check mdout.dmp.min.dif
> ---------------------
> 16) cd pbsa_pgb; ./Run.pbpgb.min
> diffing mdout.pbpgb.min.save with mdout.pbpgb.min
> possible FAILURE: check mdout.pbpgb.min.dif
>
> Thank you for your time and help.
> Msgr. E. Joseph Nolan IV
>
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Received on Tue Feb 08 2005 - 20:53:01 PST
