Sun Oct 9 16:45:40 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 Sun Oct 9 2011 at 16:45:40 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2400 !!! WARNING: ASL 45 has a net charge of -0.1000 !!! WARNING: GLM 51 has a net charge of -0.0940 !!! WARNING: GLM 123 has a net charge of -0.0940 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: 0.6609606 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): -55.48900 -6.820000 ymin,ymax (A): -13.67200 34.58100 zmin,zma (A): -3.690000 50.17100 x,y,z range (A): 48.66900 48.25300 53.86100 scale (grids/A): 0.6609606 object centre (A): -31.15450 10.45450 23.24050 number of atom coordinates read : 2400 total number of charged atoms : 2317 net assigned charge : -1.287996 assigned positive charge : 358.9500 centred at (gu) : 88.86195 91.10029 88.75507 assigned negative charge : -360.2389 centred at (gu) : 88.89630 91.00732 88.89101 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7292 nv = 96 ne = 84 npr = 47218 no. pairs analyzed = 47218 no. exposed pairs = 3135 no. arc points = 22209 no. surface atoms = 1061 nbur = 1339 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 437 mr = 3905 m= 3 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2137 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8495 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7670955E-08 -2.2996932E-08 midg,1,midg; midg,igrid,midg -1.7151615E-08 1.6868224E-08 1,midg,midg; igrid,midg,midg 3.1782479E-09 -8.2510869E-09 gauss-seidel spectral radius is 0.9881256 estimated iterations to convergence 75 setup time was (sec) 0.5000000 now iterating at: 16:45:41 rms-change max change #iterations 0.1608690 25.80129 at 10iterations 1.7188616E-02 2.570042 at 20iterations 1.8020615E-03 0.2584610 at 30iterations 1.9566703E-04 3.0315399E-02 at 40iterations 2.2923647E-05 3.5400391E-03 at 50iterations finished qdiffx linear iterations at : 16:45:43 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 2.2923647E-05 3.5400391E-03 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 16:45:44 3.110u 0.128s 0:03.56 90.7% 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 Sun Oct 9 2011 at 16:45:44 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2400 !!! WARNING: ASL 45 has a net charge of -0.1000 !!! WARNING: GLM 51 has a net charge of -0.0940 !!! WARNING: GLM 123 has a net charge of -0.0940 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: 1.982882 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): -55.48900 -6.820000 ymin,ymax (A): -13.67200 34.58100 zmin,zma (A): -3.690000 50.17100 x,y,z range (A): 48.66900 48.25300 53.86100 scale (grids/A): 1.982882 object centre (A): -31.15450 10.45450 23.24050 number of atom coordinates read : 2400 total number of charged atoms : 2317 net assigned charge : -1.287996 assigned positive charge : 358.9500 centred at (gu) : 86.58533 93.30016 86.26479 assigned negative charge : -360.2389 centred at (gu) : 86.68855 93.02216 86.67294 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 77929 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22209 grid for indexing accessible points = 1.400000 m= 28971 mr = 53424 m= 5103 mr = 21126 m= 379 mr = 3284 m= 10 mr = 174 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 34384 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 18337 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) : 0.6609606 object centre at (A) : -31.15450 10.45450 23.24050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1903551E-02 -4.0020407E-03 midg,1,midg; midg,igrid,midg -3.1700707E-03 -4.8823073E-03 1,midg,midg; igrid,midg,midg 4.9079475E-03 -2.5803940E-02 gauss-seidel spectral radius is 0.9987261 estimated iterations to convergence 222 setup time was (sec) 0.8200000 now iterating at: 16:45:45 rms-change max change #iterations 4.447888 195.6663 at 10iterations 2.135278 71.61385 at 20iterations 1.024919 30.14256 at 30iterations 0.4941837 17.86516 at 40iterations 0.2376554 6.944611 at 50iterations 0.1141291 3.414692 at 60iterations 5.4904740E-02 1.759213 at 70iterations 2.6438259E-02 0.8913984 at 80iterations 1.2702223E-02 0.3832474 at 90iterations 6.1351997E-03 0.1875563 at 100iterations 2.9570961E-03 8.6960793E-02 at 110iterations 1.4181799E-03 4.6954155E-02 at 120iterations finished qdiffx linear iterations at : 16:45:51 total time elapsed so far: 6.790000 # loops : 120 mean,max change (kT/e) : 1.4181799E-03 4.6954155E-02 energy calculations done at 6.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.960000 DelPhi exited at 16:45:51 6.958u 0.151s 0:07.37 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 Oct 9 2011 at 16:45:51 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2400 !!! WARNING: ASL 45 has a net charge of -0.1000 !!! WARNING: GLM 51 has a net charge of -0.0940 !!! WARNING: GLM 123 has a net charge of -0.0940 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: 2.974323 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): -55.48900 -6.820000 ymin,ymax (A): -13.67200 34.58100 zmin,zma (A): -3.690000 50.17100 x,y,z range (A): 48.66900 48.25300 53.86100 scale (grids/A): 2.974323 object centre (A): -31.15450 10.45450 23.24050 number of atom coordinates read : 2400 total number of charged atoms : 2317 net assigned charge : -1.287996 assigned positive charge : 358.9500 centred at (gu) : 84.87775 94.95020 84.39704 assigned negative charge : -360.2389 centred at (gu) : 85.03279 94.53308 85.00937 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 180132 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22209 grid for indexing accessible points = 1.400000 m= 91436 mr = 129702 m= 35434 mr = 73952 m= 9542 mr = 28465 m= 1549 mr = 7257 m= 151 mr = 1049 m= 1 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.8000001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.350000 number of dielectric boundary points 77732 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 18536 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) : 1.982882 object centre at (A) : -31.15450 10.45450 23.24050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5108750E-02 8.3284929E-02 midg,1,midg; midg,igrid,midg 8.0753275E-04 -9.4971634E-02 1,midg,midg; igrid,midg,midg -2.0292521E-02 -0.3168952 gauss-seidel spectral radius is 0.9992864 estimated iterations to convergence 295 setup time was (sec) 1.640000 now iterating at: 16:45:53 rms-change max change #iterations 10.32982 431.0338 at 10iterations 6.121969 161.5747 at 20iterations 3.600355 83.90590 at 30iterations 2.119519 42.31695 at 40iterations 1.239463 28.72896 at 50iterations 0.7260740 12.83630 at 60iterations 0.4237283 7.808975 at 70iterations 0.2477759 4.364578 at 80iterations 0.1445008 2.578632 at 90iterations 8.4143028E-02 1.643203 at 100iterations 4.9049076E-02 0.9051919 at 110iterations 2.8541971E-02 0.5002353 at 120iterations 1.6640732E-02 0.2847548 at 130iterations 9.6664261E-03 0.1720266 at 140iterations 5.6025810E-03 0.1021819 at 150iterations 3.2642861E-03 5.6289673E-02 at 160iterations 1.8980304E-03 3.7597656E-02 at 170iterations 1.1005496E-03 1.9068360E-02 at 180iterations finished qdiffx linear iterations at : 16:46:03 total time elapsed so far: 11.07000 # loops : 180 mean,max change (kT/e) : 1.1005496E-03 1.9068360E-02 energy calculations done at 11.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.24000 DelPhi exited at 16:46:03 11.240u 0.156s 0:11.65 97.7% 0+0k 0+0io 0pf+0w