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

From: Anthony Cruz <acb15885.uprm.edu>
Date: Fri, 9 Sep 2005 13:19:12 -0600

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
==============================================================
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Received on Fri Sep 09 2005 - 18:53:00 PDT