Sat Oct 8 18:39:28 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 18:39:28 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 = 2594 !!! 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6141213 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): -31.79500 17.56500 ymin,ymax (A): -23.50300 22.92000 zmin,zma (A): -12.58400 45.38500 x,y,z range (A): 49.36000 46.42300 57.96900 scale (grids/A): 0.6141213 object centre (A): -7.115000 -0.2915001 16.40050 number of atom coordinates read : 2594 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 88.44966 89.22952 89.68052 assigned negative charge : -387.9385 centred at (gu) : 88.35326 89.26038 89.56392 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6327 nv = 96 ne = 84 npr = 54104 no. pairs analyzed = 54104 no. exposed pairs = 2930 no. arc points = 20840 no. surface atoms = 999 nbur = 1595 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 324 mr = 3604 m= 2 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 74 time to turn everything in is 0.2900000 number of dielectric boundary points 3001 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2009 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7828 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1622030E-09 8.5104608E-09 midg,1,midg; midg,igrid,midg 5.2609077E-09 8.5869672E-10 1,midg,midg; igrid,midg,midg -3.9310044E-09 5.7114993E-09 gauss-seidel spectral radius is 0.9862648 estimated iterations to convergence 70 setup time was (sec) 0.5300000 now iterating at: 18:39:28 rms-change max change #iterations 0.1247013 22.88463 at 10iterations 1.0943997E-02 1.814224 at 20iterations 9.8515057E-04 0.1385670 at 30iterations 8.8496738E-05 1.4549255E-02 at 40iterations 8.2827246E-06 1.1577606E-03 at 50iterations finished qdiffx linear iterations at : 18:39:31 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 8.2827246E-06 1.1577606E-03 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 18:39:32 3.286u 0.176s 0:03.73 92.4% 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 18:39:32 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 = 2594 !!! 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.842364 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): -31.79500 17.56500 ymin,ymax (A): -23.50300 22.92000 zmin,zma (A): -12.58400 45.38500 x,y,z range (A): 49.36000 46.42300 57.96900 scale (grids/A): 1.842364 object centre (A): -7.115000 -0.2915001 16.40050 number of atom coordinates read : 2594 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 85.34853 87.68832 89.04144 assigned negative charge : -387.9385 centred at (gu) : 85.05971 87.78079 88.69165 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69564 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20840 grid for indexing accessible points = 1.400000 m= 24233 mr = 49132 m= 3338 mr = 18174 m= 175 mr = 2057 m= 0 mr = 79 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 5917 time to turn everything in is 0.5000000 number of dielectric boundary points 27868 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 142 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 19181 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) : 0.6141213 object centre at (A) : -7.115000 -0.2915001 16.40050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6186059E-02 2.1588143E-02 midg,1,midg; midg,igrid,midg 1.1074453E-02 2.1965150E-03 1,midg,midg; igrid,midg,midg -5.6493673E-03 2.7823690E-02 gauss-seidel spectral radius is 0.9985366 estimated iterations to convergence 207 setup time was (sec) 0.7800000 now iterating at: 18:39:33 rms-change max change #iterations 3.970353 158.8568 at 10iterations 1.804616 64.02647 at 20iterations 0.8216219 28.11869 at 30iterations 0.3765966 12.32473 at 40iterations 0.1716090 6.178237 at 50iterations 7.8490466E-02 2.529175 at 60iterations 3.5755385E-02 1.404343 at 70iterations 1.6282411E-02 0.5390472 at 80iterations 7.4554603E-03 0.2336521 at 90iterations 3.3973402E-03 0.1076012 at 100iterations 1.5540376E-03 5.1956177E-02 at 110iterations 7.0978410E-04 2.2612572E-02 at 120iterations finished qdiffx linear iterations at : 18:39:39 total time elapsed so far: 7.190000 # loops : 120 mean,max change (kT/e) : 7.0978410E-04 2.2612572E-02 energy calculations done at 7.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.370000 DelPhi exited at 18:39:39 7.371u 0.210s 0:07.87 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 Sat Oct 8 2011 at 18:39:39 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 = 2594 !!! 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.763546 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): -31.79500 17.56500 ymin,ymax (A): -23.50300 22.92000 zmin,zma (A): -12.58400 45.38500 x,y,z range (A): 49.36000 46.42300 57.96900 scale (grids/A): 2.763546 object centre (A): -7.115000 -0.2915001 16.40050 number of atom coordinates read : 2594 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 83.02258 86.53227 88.56189 assigned negative charge : -387.9385 centred at (gu) : 82.58945 86.67113 88.03730 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 161183 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20840 grid for indexing accessible points = 1.400000 m= 80708 mr = 118939 m= 27132 mr = 66987 m= 5871 mr = 21944 m= 781 mr = 4431 m= 46 mr = 541 m= 0 mr = 23 time to grow re-entrant surface = 0.6800001 no. cavity mid-points inaccessible to solvent = 19679 time to turn everything in is 1.210000 number of dielectric boundary points 62856 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 19595 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) : 1.842364 object centre at (A) : -7.115000 -0.2915001 16.40050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1210158 0.2685677 midg,1,midg; midg,igrid,midg 0.1523221 2.2278048E-02 1,midg,midg; igrid,midg,midg -5.7454903E-02 0.3689289 gauss-seidel spectral radius is 0.9992234 estimated iterations to convergence 283 setup time was (sec) 1.510000 now iterating at: 18:39:41 rms-change max change #iterations 9.333051 297.0197 at 10iterations 5.338123 113.9575 at 20iterations 3.034658 63.22779 at 30iterations 1.728802 35.56616 at 40iterations 0.9807960 19.32602 at 50iterations 0.5581715 10.39968 at 60iterations 0.3159659 6.132767 at 70iterations 0.1787414 3.595278 at 80iterations 0.1013081 1.975487 at 90iterations 5.7447761E-02 1.030489 at 100iterations 3.2515995E-02 0.5875111 at 110iterations 1.8440431E-02 0.3293457 at 120iterations 1.0431178E-02 0.2041130 at 130iterations 5.9169484E-03 0.1119289 at 140iterations 3.3515114E-03 6.3909531E-02 at 150iterations 1.8991650E-03 3.8963318E-02 at 160iterations 1.0744747E-03 2.0704269E-02 at 170iterations 6.0779776E-04 1.2016296E-02 at 180iterations finished qdiffx linear iterations at : 18:39:51 total time elapsed so far: 11.74000 # loops : 180 mean,max change (kT/e) : 6.0779776E-04 1.2016296E-02 energy calculations done at 11.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.91000 DelPhi exited at 18:39:52 11.913u 0.229s 0:12.43 97.5% 0+0k 0+0io 0pf+0w