AMBER Archive (2005)

Subject: AMBER: amber compilation on SGI ALTIX 350 (TEST FAILD)

From: Anthony Cruz (acb15885_at_uprm.edu)
Date: Fri Sep 09 2005 - 14:19:12 CDT


Hi USERS:

Today I compile AMBER on a SGI ALTIX 350. I patch the source with the
bugfix.all but one of the patch could not be apply because the file could not
be found and ask for a file to apply the patch (Bugfix 50). When I test the
serial compilation o have the fallowing errors, I paste the massage and the
diff file. The errors are crytical???? How to resolve the problems???

Sorry for the long mail...

Thanks
Anthony

==============================================================
cd tgtmd/change_target.ntr; ./Run.tgtmd
SANDER: Targeted MD with changing target and restraints
diffing tgtmd.out.save with tgtmd.out
possible FAILURE: check tgtmd.out.dif
==============================================================
252c252
< 1-4 NB = 15.4663 1-4 EEL = 222.0190 VDWAALS =
-2.8236

---
>  1-4 NB =        15.4663  1-4 EEL =       222.0191  VDWAALS    =        
-2.8236
264c264
<  EELEC  =      -238.2734  EHBOND  =         0.0000  RESTRAINT  =         
9.4654
---
>  EELEC  =      -238.2734  EHBOND  =         0.0000  RESTRAINT  =         
9.4655
276c276
<  EAMBER (non-restraint)  =         3.5135
---
>  EAMBER (non-restraint)  =         3.5134
284c284
<  BOND   =         8.8448  ANGLE   =        16.5235  DIHED      =        
15.2613
---
>  BOND   =         8.8448  ANGLE   =        16.5235  DIHED      =        
15.2614
287c287
<  EAMBER (non-restraint)  =         4.6734
---
>  EAMBER (non-restraint)  =         4.6733
293c293
<  NSTEP =      900   TIME(PS) =       1.800  TEMP(K) =   466.94  PRESS =     
0.0
---
>  NSTEP =      900   TIME(PS) =       1.800  TEMP(K) =   466.93  PRESS =     
0.0
306c306
<  BOND   =         6.6787  ANGLE   =        17.6617  DIHED      =        
14.1099
---
>  BOND   =         6.6787  ANGLE   =        17.6618  DIHED      =        
14.1099
316c316
<  Etot   =        62.5577  EKtot   =        41.5381  EPtot      =        
21.0196
---
>  Etot   =        62.5577  EKtot   =        41.5381  EPtot      =        
21.0195

============================================================== cd tgtmd/PME; ./Run.tgtPME SANDER: Targeted MD with PME diffing tgtmd.out.save with tgtmd.out possible FAILURE: check tgtmd.out.dif ============================================================== 192c192 < Etot = -4879.0818 EKtot = 656.7986 EPtot = -5535.8804 --- > Etot = -4879.0817 EKtot = 656.7986 EPtot = -5535.8804 ============================================================== cd pheTI; ./Run.0; ./Run.1; ./Run.p0; ./Run.p1 diffing out.0.save with out.0 PASSED ============================================================== diffing out.p1.save with out.p1 possible FAILURE: check out.p1.dif ============================================================== 190c190 < Ewald error estimate: 0.5094E-16 --- > Ewald error estimate: 0.0000 ============================================================== cd qmmm/standard; ./Run.lysine diffing lysine.out.save with lysine.out possible FAILURE: check lysine.out.dif ============================================================== 71c71 < 10 -2.1110E-1 9.5830E-1 4.1484 CG 8 --- > 10 -2.1110E-1 9.5830E-1 4.1485 CG 8 83c83 < 20 -6.5331E-1 9.8858E-1 2.8940 N 1 --- > 20 -6.5331E-1 9.8860E-1 2.8941 N 1 91c91 < 20 -6.5331E-1 9.8858E-1 2.8940 N 1 --- > 20 -6.5331E-1 9.8860E-1 2.8941 N 1

============================================================== cd antechamber/tp; ./Run.tp Running: /home/asantana/amber/amber8/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full

Running: /home/asantana/amber/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

Total number of electrons: 58; net charge: 0

Running: /home/asantana/amber/amber8/exe/divcon

Running: /home/asantana/amber/amber8/exe/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /home/asantana/amber/amber8/dat/antechamber/BCCPARM.DAT -s 2 -j 1

Running: /home/asantana/amber/amber8/exe/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC

Running: /home/asantana/amber/amber8/exe/atomtype -i ANTECHAMBER_PREP.AC0 -o ANTECHAMBER_PREP.AC -p gaff

Running: /home/asantana/amber/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 ============================================================== 10c10 < 4 CG ca M 3 2 1 1.5 111.2 180.0 -0.118 --- > 4 CG ca M 3 2 1 1.5 111.2 -180.0 -0.118

============================================================== diffing prmtop.save with prmtop possible FAILURE: check prmtop.dif ============================================================== 15c15 < -2.15 2.61 -2.07 2.45 -2.49 --- > -2.16 2.60 -2.07 2.45 -2.49 17c17 < 3.00E-1 -4.64 3.48 --- > 2.97E-1 -4.63 3.48

============================================================== cd antechamber/tp; ./Run.tp_mol2 Running: /home/asantana/amber/amber8/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full

Running: /home/asantana/amber/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

Total number of electrons: 58; net charge: 0

Running: /home/asantana/amber/amber8/exe/divcon

Running: /home/asantana/amber/amber8/exe/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /home/asantana/amber/amber8/dat/antechamber/BCCPARM.DAT -s 2 -j 1

Running: /home/asantana/amber/amber8/exe/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC

diffing tp.mol2.save with tp.mol2 PASSED ============================================================== diffing prmtop.mol2.save with prmtop.mol2 possible FAILURE: check prmtop.mol2.dif ============================================================== 15,16c15,16 < -2.15 -2.07 3.00E-1 -2.49 -2.64 < -2.04 2.35 -4.64 3.48 2.45 --- > -2.16 -2.07 2.97E-1 -2.49 -2.64 > -2.04 2.35 -4.63 3.48 2.45

============================================================== cd antechamber/ash; ./Run.ash Running: /home/asantana/amber/amber8/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full

Running: /home/asantana/amber/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

Total number of electrons: 100; net charge: 0

Running: /home/asantana/amber/amber8/exe/divcon

Running: /home/asantana/amber/amber8/exe/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /home/asantana/amber/amber8/dat/antechamber/BCCPARM.DAT -s 2 -j 1

Running: /home/asantana/amber/amber8/exe/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC

Running: /home/asantana/amber/amber8/exe/atomtype -i ANTECHAMBER_PREP.AC0 -o ANTECHAMBER_PREP.AC -p gaff

Running: /home/asantana/amber/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 ============================================================== 10,11c10,11 < 4 CH3 c3 M 3 2 1 1. 111. 180. -0.17 < 5 HH31 hc E 4 3 2 1. 90. 0. 0.08 --- > 4 CH3 c3 M 3 2 1 1. 111. -180. -0.17 > 5 HH31 hc E 4 3 2 1. 90. 0. 0.07 15c15 < 9 O o E 8 4 3 1. 120. 180. -0.61 --- > 9 O o E 8 4 3 1. 120. 180. -0.60 18,20c18,20 < 12 CA c3 M 10 8 4 1. 121. 180. 0.05 < 13 HA h1 E 12 10 8 1. 109. -60. 0.10 < 14 C2 c B 12 10 8 1. 111. -180. 0.64 --- > 12 CA c3 M 10 8 4 1. 121. 180. 0.04 > 13 HA h1 E 12 10 8 1. 109. -60. 0.11 > 14 C2 c B 12 10 8 1. 111. -180. 0.63 22c22 < 16 N1 n B 14 12 10 1. 116. 180. -0.55 --- > 16 N1 n B 14 12 10 1. 116. -180. -0.55 26c26 < 20 H2 h1 E 18 16 14 1. 109. 120. 0.04 --- > 20 H2 h1 E 18 16 14 1. 109. 120. 0.03 28,29c28,29 < 22 CB c3 M 12 10 8 1. 111. 60. -0.15 < 23 HB2 hc E 22 12 10 1. 109. -60. 0.11 --- > 22 CB c3 M 12 10 8 1. 111. 60. -0.14 > 23 HB2 hc E 22 12 10 1. 109. -60. 0.10

============================================================== diffing frcmod.save with frcmod PASSED ============================================================== diffing leap.out.save with leap.out PASSED ============================================================== diffing prmtop.save with prmtop possible FAILURE: check prmtop.dif ============================================================== 17,19c17,19 < -1.1E+1 -1.0E+1 6.1 9.4E-1 1.8 < 1.1E+1 -1.1E+1 -1.0E+1 6.1 1.4 < 1.3 7.4E-1 4.9E-1 -2.8 2.0 --- > -1.1E+1 -1.0E+1 6.0 7.9E-1 2.0 > 1.1E+1 -1.1E+1 -1.0E+1 6.1 1.3 > 1.3 6.9E-1 5.0E-1 -2.6 1.9

============================================================== cd antechamber/sustiva; ./Run.sustiva Running: /home/asantana/amber/amber8/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full

Running: /home/asantana/amber/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

Total number of electrons: 160; net charge: 0

Running: /home/asantana/amber/amber8/exe/divcon

Running: /home/asantana/amber/amber8/exe/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /home/asantana/amber/amber8/dat/antechamber/BCCPARM.DAT -s 2 -j 1

Running: /home/asantana/amber/amber8/exe/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC

Running: /home/asantana/amber/amber8/exe/atomtype -i ANTECHAMBER_PREP.AC0 -o ANTECHAMBER_PREP.AC -p gaff

Running: /home/asantana/amber/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 ============================================================== 10c10 < 4 C2 ca M 3 2 1 1.5 111.2 180.0 -0.178 --- > 4 C2 ca M 3 2 1 1.5 111.2 -180.0 -0.178 24,25c24,25 < 18 O1 os M 16 14 13 1.3 115.7 -5.6 -0.376 < 19 C3 c3 M 18 16 14 1.4 124.5 -18.7 0.315 --- > 18 O1 os M 16 14 13 1.3 115.7 -5.6 -0.375 > 19 C3 c3 M 18 16 14 1.4 124.5 -18.7 0.314 27c27 < 21 F1 f E 20 19 18 1.3 110.0 61.2 -0.228 --- > 21 F1 f E 20 19 18 1.3 110.0 61.2 -0.229 30c30 < 24 C4 c1 M 19 18 16 1.4 107.2 154.8 -0.197 --- > 24 C4 c1 M 19 18 16 1.4 107.2 154.8 -0.196

============================================================== diffing prmtop.save with prmtop possible FAILURE: check prmtop.dif ============================================================== 16,17c16,17 < -3.24 -9.05E-1 3.08 -3.48E-1 -1.36 < -1.21 2.85 -3.14 2.72 1.98 --- > -3.25 -9.01E-1 3.08 -3.49E-1 -1.36 > -1.21 2.85 -3.14 2.72 1.97 19,21c19,21 < 5.74 1.12E+1 -4.17 -4.20 -3.91 < -3.59 2.49E-1 -1.43 1.97 -1.95 < 1.46 1.50 -2.04 1.44 1.47 --- > 5.73 1.12E+1 -4.17 -4.20 -3.91 > -3.58 2.43E-1 -1.43 1.97 -1.95 > 1.46 1.51 -2.05 1.44 1.47

============================================================== 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: /home/asantana/amber/amber8/exe/divcon

diffing fluorescein.prepin.save with fluorescein.prepin possible FAILURE: check fluorescein.prepin.dif ============================================================== 10c10 < 4 C1 ca M 3 2 1 1.5 111.2 180.0 -0.437 --- > 4 C1 ca M 3 2 1 1.5 111.2 -180.0 -0.437 39,40c39,40 < 33 C23 ca M 31 29 27 1.3 119.4 -0.0 -0.118 < 34 H33 ha E 33 31 29 1.0 121.3 -179.9 0.155 --- > 33 C23 ca M 31 29 27 1.3 119.4 -0.0 -0.117 > 34 H33 ha E 33 31 29 1.0 121.3 -179.9 0.156 ============================================================== diffing prmtop.save with prmtop possible FAILURE: check prmtop.dif ============================================================== 17c17 < 2.0 9.1E-3 2.2 -5.7 8.0 --- > 2.0 9.2E-3 2.2 -5.7 8.0

============================================================== cd antechamber/guanine; ./Run.guanine Running: /home/asantana/amber/amber8/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full

Running: /home/asantana/amber/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

Total number of electrons: 140; net charge: 0

Running: /home/asantana/amber/amber8/exe/divcon

Running: /home/asantana/amber/amber8/exe/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /home/asantana/amber/amber8/dat/antechamber/BCCPARM.DAT -s 2 -j 1

Running: /home/asantana/amber/amber8/exe/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC

Running: /home/asantana/amber/amber8/exe/atomtype -i ANTECHAMBER_PREP.AC0 -o ANTECHAMBER_PREP.AC -p gaff

Running: /home/asantana/amber/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 ============================================================== 10c10 < 4 O5' oh M 3 2 1 1. 111. 180. -0.62 --- > 4 O5' oh M 3 2 1 1. 111. -180. -0.61 17c17 < 11 C3' c3 3 9 6 4 1. 115. 30. 0.11 --- > 11 C3' c3 3 9 6 4 1. 115. 30. 0.12

============================================================== diffing prmtop.save with prmtop possible FAILURE: check prmtop.dif ============================================================== 16c16 < -1.1E+1 7.5 2.0 9.8E-1 7.0E-1 --- > -1.1E+1 7.5 2.0 9.9E-1 6.9E-1 21,22c21,22 < 6.0 1.2E+1 -1.6E+1 7.4 7.8 < -1.2E+1 2.1 --- > 6.0 1.2E+1 -1.6E+1 7.4 7.7 > -1.2E+1 2.0

============================================================== cd antechamber/guanine_amber; ./Run.guanine_amber Running: /home/asantana/amber/amber8/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full

Running: /home/asantana/amber/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p amber

Total number of electrons: 140; net charge: 0

Running: /home/asantana/amber/amber8/exe/divcon

Running: /home/asantana/amber/amber8/exe/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /home/asantana/amber/amber8/dat/antechamber/BCCPARM.DAT -s 2 -j 1

Running: /home/asantana/amber/amber8/exe/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC

Running: /home/asantana/amber/amber8/exe/atomtype -i ANTECHAMBER_PREP.AC0 -o ANTECHAMBER_PREP.AC -p amber

Running: /home/asantana/amber/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 ============================================================== 10,12c10,12 < 4 O5' OH M 3 2 1 1.5 111.2 180.0 -0.620 < 5 H5T HO E 4 3 2 0.9 84.5 76.6 0.414 < 6 C5' CT M 4 3 2 1.4 35.6 -117.6 0.115 --- > 4 O5' OH M 3 2 1 1.5 111.2 -180.0 -0.619 > 5 H5T HO E 4 3 2 0.9 84.5 76.6 0.413 > 6 C5' CT M 4 3 2 1.4 35.6 -117.6 0.114 15,19c15,19 < 9 C4' CT M 6 4 3 1.5 109.9 163.6 0.134 < 10 H4' H1 E 9 6 4 1.0 109.4 159.9 0.093 < 11 C3' CT 3 9 6 4 1.5 115.7 30.9 0.119 < 12 H3' H1 E 11 9 6 1.0 109.5 29.9 0.077 < 13 C2' CT B 11 9 6 1.5 102.7 -86.3 -0.149 --- > 9 C4' CT M 6 4 3 1.5 109.9 163.6 0.135 > 10 H4' H1 E 9 6 4 1.0 109.4 159.9 0.094 > 11 C3' CT 3 9 6 4 1.5 115.7 30.9 0.120 > 12 H3' H1 E 11 9 6 1.0 109.5 29.9 0.076 > 13 C2' CT B 11 9 6 1.5 102.7 -86.3 -0.148 21c21 < 15 H2'2 HC E 13 11 9 1.0 109.5 -119.9 0.076 --- > 15 H2'2 HC E 13 11 9 1.0 109.5 -119.9 0.075 27,28c27,28 < 21 N9 N* M 19 18 9 1.4 108.0 -127.6 -0.221 < 22 C8 CK M 21 19 18 1.3 129.2 81.5 0.406 --- > 21 N9 N* M 19 18 9 1.4 108.0 -127.6 -0.220 > 22 C8 CK M 21 19 18 1.3 129.2 81.5 0.407 30,31c30,31 < 24 N7 NB M 22 21 19 1.3 114.0 -179.8 -0.595 < 25 C5 CB M 24 22 21 1.3 103.8 0.0 0.177 --- > 24 N7 NB M 22 21 19 1.3 114.0 -179.8 -0.596 > 25 C5 CB M 24 22 21 1.3 103.8 0.0 0.178 34c34 < 28 N1 NA M 26 25 24 1.4 111.4 -179.9 -0.508 --- > 28 N1 NA M 26 25 24 1.4 111.4 -179.9 -0.507 36c36 < 30 C2 CA M 28 26 25 1.3 125.2 -0.1 0.678 --- > 30 C2 CA M 28 26 25 1.3 125.2 -0.1 0.677 41c41 < 35 C4 CB M 34 30 28 1.3 112.1 -0.0 0.116 --- > 35 C4 CB M 34 30 28 1.3 112.1 -0.0 0.115

============================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu