Mon Oct 10 17:01:52 PDT 2011 #!/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+sph2.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 = amb2.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 Mon Oct 10 2011 at 17:01:52 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 # of charge parameter records: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2950 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6303228 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): -8.899000 47.58000 ymin,ymax (A): -6.903000 42.18600 zmin,zma (A): 0.8850001 55.45500 x,y,z range (A): 56.47900 49.08900 54.57000 scale (grids/A): 0.6303228 object centre (A): 19.34050 17.64150 28.17000 number of atom coordinates read : 2950 total number of charged atoms : 2809 net assigned charge : -4.985966 assigned positive charge : 446.6439 centred at (gu) : 89.71875 89.33357 88.61681 assigned negative charge : -451.6311 centred at (gu) : 89.68134 89.23787 88.50143 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7836 nv = 96 ne = 84 npr = 59642 no. pairs analyzed = 59642 no. exposed pairs = 3882 no. arc points = 27219 no. surface atoms = 1303 nbur = 1647 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 382 mr = 4087 m= 0 mr = 41 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 39 time to turn everything in is 0.3400000 number of dielectric boundary points 4090 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2745 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9548 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3413387E-08 4.8245394E-09 midg,1,midg; midg,igrid,midg -1.7571193E-08 3.9617682E-09 1,midg,midg; igrid,midg,midg -9.6316475E-09 -1.2564777E-09 gauss-seidel spectral radius is 0.9869980 estimated iterations to convergence 72 setup time was (sec) 0.5600000 now iterating at: 17:01:53 rms-change max change #iterations 0.1471205 23.99791 at 10iterations 1.4005985E-02 2.145267 at 20iterations 1.3427803E-03 0.1811752 at 30iterations 1.2601088E-04 1.5861511E-02 at 40iterations 1.2366114E-05 1.6193390E-03 at 50iterations finished qdiffx linear iterations at : 17:01:56 total time elapsed so far: 3.030000 # loops : 50 mean,max change (kT/e) : 1.2366114E-05 1.6193390E-03 energy calculations done at 3.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.210000 DelPhi exited at 17:01:57 3.211u 0.147s 0:04.19 79.9% 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 Mon Oct 10 2011 at 17:01:57 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 # of charge parameter records: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2950 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.890968 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): -8.899000 47.58000 ymin,ymax (A): -6.903000 42.18600 zmin,zma (A): 0.8850001 55.45500 x,y,z range (A): 56.47900 49.08900 54.57000 scale (grids/A): 1.890968 object centre (A): 19.34050 17.64150 28.17000 number of atom coordinates read : 2950 total number of charged atoms : 2809 net assigned charge : -4.985966 assigned positive charge : 446.6439 centred at (gu) : 89.15508 88.00003 85.84943 assigned negative charge : -451.6311 centred at (gu) : 89.04393 87.71331 85.50409 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 84342 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27219 grid for indexing accessible points = 1.400000 m= 28812 mr = 56858 m= 4126 mr = 20420 m= 214 mr = 2394 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1120 time to turn everything in is 0.6200000 number of dielectric boundary points 37765 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 175 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 22084 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) : 0.6303228 object centre at (A) : 19.34050 17.64150 28.17000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7195097E-03 1.5483279E-02 midg,1,midg; midg,igrid,midg -2.9250799E-02 6.1218039E-04 1,midg,midg; igrid,midg,midg -5.9528641E-02 1.5907686E-02 gauss-seidel spectral radius is 0.9986535 estimated iterations to convergence 216 setup time was (sec) 0.8900000 now iterating at: 17:01:58 rms-change max change #iterations 4.557666 182.4118 at 10iterations 2.139953 74.08269 at 20iterations 1.005782 32.83919 at 30iterations 0.4720926 15.17052 at 40iterations 0.2219811 6.725006 at 50iterations 0.1042194 3.250847 at 60iterations 4.9110305E-02 1.364811 at 70iterations 2.3024464E-02 0.6815567 at 80iterations 1.0830509E-02 0.3221817 at 90iterations 5.0891014E-03 0.1540251 at 100iterations 2.4031585E-03 7.1155548E-02 at 110iterations 1.1286931E-03 3.3469200E-02 at 120iterations finished qdiffx linear iterations at : 17:02:04 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 1.1286931E-03 3.3469200E-02 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 17:02:06 7.695u 0.178s 0:08.92 88.1% 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 Mon Oct 10 2011 at 17:02:06 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 # of charge parameter records: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2950 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.836452 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): -8.899000 47.58000 ymin,ymax (A): -6.903000 42.18600 zmin,zma (A): 0.8850001 55.45500 x,y,z range (A): 56.47900 49.08900 54.57000 scale (grids/A): 2.836452 object centre (A): 19.34050 17.64150 28.17000 number of atom coordinates read : 2950 total number of charged atoms : 2809 net assigned charge : -4.985966 assigned positive charge : 446.6439 centred at (gu) : 88.73256 86.99978 83.77395 assigned negative charge : -451.6311 centred at (gu) : 88.56579 86.56992 83.25615 start vw surface at 0.1600000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 195389 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27219 grid for indexing accessible points = 1.400000 m= 94344 mr = 138799 m= 32285 mr = 75137 m= 7224 mr = 25285 m= 884 mr = 5135 m= 48 mr = 556 m= 0 mr = 20 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 3566 time to turn everything in is 1.450000 number of dielectric boundary points 85242 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 22471 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) : 1.890968 object centre at (A) : 19.34050 17.64150 28.17000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2965080 0.1177851 midg,1,midg; midg,igrid,midg -0.2620514 3.1128954E-02 1,midg,midg; igrid,midg,midg -0.7256044 0.3370870 gauss-seidel spectral radius is 0.9992882 estimated iterations to convergence 296 setup time was (sec) 1.750000 now iterating at: 17:02:08 rms-change max change #iterations 10.99496 387.9630 at 10iterations 6.588410 150.3365 at 20iterations 3.905017 88.83371 at 30iterations 2.306166 50.47955 at 40iterations 1.355682 28.04253 at 50iterations 0.7941651 17.51600 at 60iterations 0.4646186 8.510300 at 70iterations 0.2715420 4.625435 at 80iterations 0.1585027 2.904947 at 90iterations 9.2257507E-02 1.609169 at 100iterations 5.3796511E-02 0.9027700 at 110iterations 3.1258434E-02 0.5572544 at 120iterations 1.8216386E-02 0.3272514 at 130iterations 1.0579451E-02 0.1989746 at 140iterations 6.1443229E-03 0.1059151 at 150iterations 3.5726405E-03 5.9515476E-02 at 160iterations 2.0773404E-03 3.9382935E-02 at 170iterations 1.2072808E-03 2.1011353E-02 at 180iterations finished qdiffx linear iterations at : 17:02:18 total time elapsed so far: 11.86000 # loops : 180 mean,max change (kT/e) : 1.2072808E-03 2.1011353E-02 energy calculations done at 11.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.06000 DelPhi exited at 17:02:19 12.062u 0.279s 0:13.35 92.3% 0+0k 0+0io 0pf+0w