Sun Jan 29 03:36:18 PST 2012 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Jan 29 2012 at 03:36:18 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 ! Automatically converted by prot2crg.py # of charge parameter records: 974 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3276 !!! WARNING: DIC 166 has a net charge of -0.8000 !!! WARNING: HIY 168 has a net charge of 0.2000 !!! WARNING: DIC 255 has a net charge of -0.8000 !!! WARNING: ZN1 1075 has a net charge of 1.4000 !!! WARNING: ZN2 1078 has a net charge of 2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6000033 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -59.73900 -9.891001 ymin,ymax (A): -5.847000 46.80800 zmin,zma (A): -68.98200 -9.648999 x,y,z range (A): 49.84800 52.65500 59.33300 scale (grids/A): 0.6000033 object centre (A): -34.81500 20.48050 -39.31550 number of atom coordinates read : 3276 total number of charged atoms : 3136 net assigned charge : -2.999967 assigned positive charge : 490.0169 centred at (gu) : 91.04972 89.42581 91.44183 assigned negative charge : -493.0179 centred at (gu) : 91.11830 89.63356 91.55192 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7665 nv = 96 ne = 84 npr = 67523 no. pairs analyzed = 67523 no. exposed pairs = 4123 no. arc points = 27562 no. surface atoms = 1408 nbur = 1868 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 398 mr = 4188 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3848 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2684 ## 251 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9659 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7235887E-09 -8.8692191E-09 midg,1,midg; midg,igrid,midg 9.3291099E-09 -9.6728057E-09 1,midg,midg; igrid,midg,midg 1.5072162E-09 -5.5973426E-09 gauss-seidel spectral radius is 0.9856749 estimated iterations to convergence 68 setup time was (sec) 0.4200000 now iterating at: 03:36:18 rms-change max change #iterations 0.1247564 20.16403 at 10iterations 1.0651654E-02 1.892023 at 20iterations 1.1741072E-03 0.1539516 at 30iterations 3.2979422E-04 5.7618141E-02 at 40iterations 1.5304617E-04 2.7579308E-02 at 50iterations finished qdiffx linear iterations at : 03:36:21 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 1.5304617E-04 2.7579308E-02 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 03:36:22 3.452u 0.201s 0:03.92 93.1% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Jan 29 2012 at 03:36:22 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 ! Automatically converted by prot2crg.py # of charge parameter records: 974 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3276 !!! WARNING: DIC 166 has a net charge of -0.8000 !!! WARNING: HIY 168 has a net charge of 0.2000 !!! WARNING: DIC 255 has a net charge of -0.8000 !!! WARNING: ZN1 1075 has a net charge of 1.4000 !!! WARNING: ZN2 1078 has a net charge of 2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.800010 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -59.73900 -9.891001 ymin,ymax (A): -5.847000 46.80800 zmin,zma (A): -68.98200 -9.648999 x,y,z range (A): 49.84800 52.65500 59.33300 scale (grids/A): 1.800010 object centre (A): -34.81500 20.48050 -39.31550 number of atom coordinates read : 3276 total number of charged atoms : 3136 net assigned charge : -2.999967 assigned positive charge : 490.0169 centred at (gu) : 93.14877 88.27659 94.32479 assigned negative charge : -493.0179 centred at (gu) : 93.35455 88.90028 94.65533 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 84214 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27562 grid for indexing accessible points = 1.400000 m= 29328 mr = 59273 m= 3984 mr = 20886 m= 154 mr = 2273 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 35215 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 191 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 24496 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6000033 object centre at (A) : -34.81500 20.48050 -39.31550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0684812E-03 -2.7966727E-02 midg,1,midg; midg,igrid,midg 2.8760385E-02 -7.3649059E-03 1,midg,midg; igrid,midg,midg -1.0290225E-02 -2.2798661E-02 gauss-seidel spectral radius is 0.9985374 estimated iterations to convergence 207 setup time was (sec) 0.6500000 now iterating at: 03:36:23 rms-change max change #iterations 4.333387 164.3506 at 10iterations 1.973769 67.46037 at 20iterations 0.8950613 28.71301 at 30iterations 0.4097550 13.29143 at 40iterations 0.1865637 5.695099 at 50iterations 8.5424073E-02 2.503147 at 60iterations 3.9199252E-02 1.193020 at 70iterations 1.7977525E-02 0.6073332 at 80iterations 8.2933400E-03 0.2477655 at 90iterations 3.8870249E-03 0.1164010 at 100iterations 1.8720938E-03 6.4170837E-02 at 110iterations 9.7478437E-04 3.5447121E-02 at 120iterations finished qdiffx linear iterations at : 03:36:30 total time elapsed so far: 7.860000 # loops : 120 mean,max change (kT/e) : 9.7478437E-04 3.5447121E-02 energy calculations done at 7.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 03:36:30 7.982u 0.204s 0:08.49 96.3% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Jan 29 2012 at 03:36:30 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 ! Automatically converted by prot2crg.py # of charge parameter records: 974 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3276 !!! WARNING: DIC 166 has a net charge of -0.8000 !!! WARNING: HIY 168 has a net charge of 0.2000 !!! WARNING: DIC 255 has a net charge of -0.8000 !!! WARNING: ZN1 1075 has a net charge of 1.4000 !!! WARNING: ZN2 1078 has a net charge of 2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.700015 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -59.73900 -9.891001 ymin,ymax (A): -5.847000 46.80800 zmin,zma (A): -68.98200 -9.648999 x,y,z range (A): 49.84800 52.65500 59.33300 scale (grids/A): 2.700015 object centre (A): -34.81500 20.48050 -39.31550 number of atom coordinates read : 3276 total number of charged atoms : 3136 net assigned charge : -2.999967 assigned positive charge : 490.0169 centred at (gu) : 94.72292 87.41475 96.48709 assigned negative charge : -493.0179 centred at (gu) : 95.03176 88.35040 96.98298 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 195142 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27562 grid for indexing accessible points = 1.400000 m= 97151 mr = 143923 m= 32417 mr = 78468 m= 6583 mr = 25129 m= 724 mr = 4639 m= 21 mr = 445 m= 0 mr = 5 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.060000 number of dielectric boundary points 79429 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 25086 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.800010 object centre at (A) : -34.81500 20.48050 -39.31550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6451891E-02 -0.3087164 midg,1,midg; midg,igrid,midg 0.4262486 3.8635384E-03 1,midg,midg; igrid,midg,midg -0.1566366 -0.2875198 gauss-seidel spectral radius is 0.9992400 estimated iterations to convergence 286 setup time was (sec) 1.310000 now iterating at: 03:36:32 rms-change max change #iterations 10.56551 379.9948 at 10iterations 6.210363 140.8125 at 20iterations 3.619962 89.90575 at 30iterations 2.098160 47.12803 at 40iterations 1.216923 25.16662 at 50iterations 0.7002395 13.41849 at 60iterations 0.4041068 7.039498 at 70iterations 0.2320624 4.086432 at 80iterations 0.1332308 2.494028 at 90iterations 7.6525293E-02 1.395767 at 100iterations 4.3882083E-02 0.8788757 at 110iterations 2.5185345E-02 0.4468355 at 120iterations 1.4477916E-02 0.2478466 at 130iterations 8.3276639E-03 0.1607513 at 140iterations 4.8462288E-03 8.8243484E-02 at 150iterations 2.8694889E-03 5.5688858E-02 at 160iterations 1.7638892E-03 3.6441803E-02 at 170iterations 1.1599959E-03 2.5072098E-02 at 180iterations finished qdiffx linear iterations at : 03:36:44 total time elapsed so far: 12.89000 # loops : 180 mean,max change (kT/e) : 1.1599959E-03 2.5072098E-02 energy calculations done at 12.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.03000 DelPhi exited at 03:36:44 13.029u 0.236s 0:13.54 97.8% 0+0k 0+0io 0pf+0w