AMBER Archive (2005)

Subject: AMBER: Amber8 installation test possible failures

From: Joe Nolan (spaceace13666_at_yahoo.com)
Date: Tue Feb 08 2005 - 13:55:39 CST


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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