Sat Oct 8 18:31:22 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 Sat Oct 8 2011 at 18:31:22 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 # of charge parameter records: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 0.6235440 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): -31.56400 17.39300 ymin,ymax (A): -23.55600 22.90700 zmin,zma (A): -12.66500 44.42800 x,y,z range (A): 48.95700 46.46300 57.09300 scale (grids/A): 0.6235440 object centre (A): -7.085501 -0.3245001 15.88150 number of atom coordinates read : 2581 total number of charged atoms : 2450 net assigned charge : 3.906009 assigned positive charge : 392.2441 centred at (gu) : 88.41171 89.22412 89.98025 assigned negative charge : -388.3385 centred at (gu) : 88.31135 89.26643 89.86878 start vw surface at 0.1600000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6568 nv = 96 ne = 84 npr = 53839 no. pairs analyzed = 53839 no. exposed pairs = 2941 no. arc points = 21178 no. surface atoms = 988 nbur = 1593 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 321 mr = 3732 m= 1 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 203 time to turn everything in is 0.4000000 number of dielectric boundary points 3105 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2077 ## 209 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 8035 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7012261E-09 1.1639289E-08 midg,1,midg; midg,igrid,midg 7.9345535E-09 4.3600265E-10 1,midg,midg; igrid,midg,midg -5.6001195E-09 7.7124849E-09 gauss-seidel spectral radius is 0.9866727 estimated iterations to convergence 71 setup time was (sec) 0.7400000 now iterating at: 18:31:23 rms-change max change #iterations 0.1335561 22.03017 at 10iterations 1.2331803E-02 1.905945 at 20iterations 1.1534513E-03 0.1907218 at 30iterations 1.0825496E-04 1.4892578E-02 at 40iterations 1.0244387E-05 1.6536713E-03 at 50iterations finished qdiffx linear iterations at : 18:31:27 total time elapsed so far: 4.310000 # loops : 50 mean,max change (kT/e) : 1.0244387E-05 1.6536713E-03 energy calculations done at 4.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.530000 DelPhi exited at 18:31:27 4.534u 0.383s 0:05.18 94.7% 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 Sat Oct 8 2011 at 18:31:27 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 1.870632 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): -31.56400 17.39300 ymin,ymax (A): -23.55600 22.90700 zmin,zma (A): -12.66500 44.42800 x,y,z range (A): 48.95700 46.46300 57.09300 scale (grids/A): 1.870632 object centre (A): -7.085501 -0.3245001 15.88150 number of atom coordinates read : 2581 total number of charged atoms : 2450 net assigned charge : 3.906009 assigned positive charge : 392.2441 centred at (gu) : 85.23449 87.67171 89.94051 assigned negative charge : -388.3385 centred at (gu) : 84.93378 87.79906 89.60625 start vw surface at 0.1500000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 71172 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21178 grid for indexing accessible points = 1.400000 m= 24942 mr = 50209 m= 3595 mr = 18657 m= 197 mr = 2322 m= 1 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 9639 time to turn everything in is 0.7100000 number of dielectric boundary points 28639 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 19217 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) : 0.6235440 object centre at (A) : -7.085501 -0.3245001 15.88150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4572706E-02 2.2329567E-02 midg,1,midg; midg,igrid,midg 1.2996405E-02 2.9388904E-03 1,midg,midg; igrid,midg,midg -8.6173331E-03 2.8957112E-02 gauss-seidel spectral radius is 0.9985783 estimated iterations to convergence 210 setup time was (sec) 1.030000 now iterating at: 18:31:29 rms-change max change #iterations 4.112059 167.7900 at 10iterations 1.891979 64.76744 at 20iterations 0.8742571 28.63507 at 30iterations 0.4028452 13.40430 at 40iterations 0.1858974 6.056000 at 50iterations 8.6051218E-02 2.684559 at 60iterations 3.9601907E-02 1.299290 at 70iterations 1.8353837E-02 0.6543274 at 80iterations 8.4224707E-03 0.2727776 at 90iterations 3.8910343E-03 0.1352978 at 100iterations 1.7961146E-03 5.3741455E-02 at 110iterations 8.3275768E-04 2.8671265E-02 at 120iterations finished qdiffx linear iterations at : 18:31:38 total time elapsed so far: 10.12000 # loops : 120 mean,max change (kT/e) : 8.3275768E-04 2.8671265E-02 energy calculations done at 10.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.33000 DelPhi exited at 18:31:38 10.334u 0.458s 0:11.10 97.1% 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 Sat Oct 8 2011 at 18:31:38 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 2.805948 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): -31.56400 17.39300 ymin,ymax (A): -23.55600 22.90700 zmin,zma (A): -12.66500 44.42800 x,y,z range (A): 48.95700 46.46300 57.09300 scale (grids/A): 2.805948 object centre (A): -7.085501 -0.3245001 15.88150 number of atom coordinates read : 2581 total number of charged atoms : 2450 net assigned charge : 3.906009 assigned positive charge : 392.2441 centred at (gu) : 82.85176 86.50755 89.91077 assigned negative charge : -388.3385 centred at (gu) : 82.40063 86.69844 89.40933 start vw surface at 0.1500000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 164975 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21178 grid for indexing accessible points = 1.400000 m= 82476 mr = 121359 m= 28244 mr = 68547 m= 6432 mr = 22967 m= 891 mr = 4912 m= 46 mr = 651 m= 0 mr = 20 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 32241 time to turn everything in is 1.820000 number of dielectric boundary points 64608 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 19598 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) : 1.870632 object centre at (A) : -7.085501 -0.3245001 15.88150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.1995644E-02 0.2084263 midg,1,midg; midg,igrid,midg 0.1513192 2.6787514E-02 1,midg,midg; igrid,midg,midg -6.2791251E-02 0.3889557 gauss-seidel spectral radius is 0.9992360 estimated iterations to convergence 286 setup time was (sec) 2.160000 now iterating at: 18:31:41 rms-change max change #iterations 9.576777 313.1301 at 10iterations 5.483118 128.8183 at 20iterations 3.124500 63.55933 at 30iterations 1.777169 36.17900 at 40iterations 1.012838 18.25239 at 50iterations 0.5762564 11.01589 at 60iterations 0.3278398 5.982294 at 70iterations 0.1866786 3.482439 at 80iterations 0.1062780 2.031691 at 90iterations 6.0355414E-02 1.176578 at 100iterations 3.4328315E-02 0.6246319 at 110iterations 1.9549549E-02 0.3505282 at 120iterations 1.1095424E-02 0.2128353 at 130iterations 6.3268356E-03 0.1216818 at 140iterations 3.6011117E-03 6.6596985E-02 at 150iterations 2.0455520E-03 4.7366142E-02 at 160iterations 1.1608851E-03 2.0651817E-02 at 170iterations 6.6068483E-04 1.3225555E-02 at 180iterations finished qdiffx linear iterations at : 18:31:56 total time elapsed so far: 17.19000 # loops : 180 mean,max change (kT/e) : 6.6068483E-04 1.3225555E-02 energy calculations done at 17.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.48000 DelPhi exited at 18:31:57 17.487u 0.481s 0:18.26 98.3% 0+0k 0+0io 0pf+0w