Tue Oct 11 08:25:22 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+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 Tue Oct 11 2011 at 08:25:23 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3195 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6044759 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): -11.60800 37.14800 ymin,ymax (A): -27.25600 21.31700 zmin,zma (A): -13.19500 45.69900 x,y,z range (A): 48.75600 48.57300 58.89400 scale (grids/A): 0.6044759 object centre (A): 12.77000 -2.969501 16.25200 number of atom coordinates read : 3195 total number of charged atoms : 2779 net assigned charge : -0.8599826 assigned positive charge : 444.4134 centred at (gu) : 90.16438 90.97743 92.26662 assigned negative charge : -445.2742 centred at (gu) : 89.99326 90.88191 92.14848 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6996 nv = 96 ne = 84 npr = 60445 no. pairs analyzed = 60445 no. exposed pairs = 3521 no. arc points = 24188 no. surface atoms = 1179 nbur = 2016 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 340 mr = 3940 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 60 time to turn everything in is 0.3500000 number of dielectric boundary points 3355 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2438 ## 262 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8757 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7973664E-09 8.4070120E-09 midg,1,midg; midg,igrid,midg -4.1870583E-09 4.8858073E-09 1,midg,midg; igrid,midg,midg -8.6213223E-09 7.6803648E-09 gauss-seidel spectral radius is 0.9858553 estimated iterations to convergence 69 setup time was (sec) 0.5800000 now iterating at: 08:25:23 rms-change max change #iterations 0.1153990 17.16612 at 10iterations 1.0171917E-02 1.514243 at 20iterations 9.2478184E-04 0.1340170 at 30iterations 9.0075271E-05 1.2552261E-02 at 40iterations 1.4405858E-05 1.8501282E-03 at 50iterations finished qdiffx linear iterations at : 08:25:26 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 1.4405858E-05 1.8501282E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 08:25:26 3.356u 0.135s 0:03.87 89.9% 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 Tue Oct 11 2011 at 08:25:26 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3195 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.813427 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): -11.60800 37.14800 ymin,ymax (A): -27.25600 21.31700 zmin,zma (A): -13.19500 45.69900 x,y,z range (A): 48.75600 48.57300 58.89400 scale (grids/A): 1.813427 object centre (A): 12.77000 -2.969501 16.25200 number of atom coordinates read : 3195 total number of charged atoms : 2779 net assigned charge : -0.8599826 assigned positive charge : 444.4134 centred at (gu) : 90.49233 92.93147 96.79932 assigned negative charge : -445.2742 centred at (gu) : 89.97942 92.64532 96.44516 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 76262 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24188 grid for indexing accessible points = 1.400000 m= 26760 mr = 53956 m= 3617 mr = 19783 m= 167 mr = 2166 m= 1 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 2993 time to turn everything in is 0.5600000 number of dielectric boundary points 30857 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 21647 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) : 0.6044759 object centre at (A) : 12.77000 -2.969501 16.25200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.5041235E-02 8.3831977E-03 midg,1,midg; midg,igrid,midg -7.7716499E-03 1.9325669E-03 1,midg,midg; igrid,midg,midg -5.7449210E-03 3.4659203E-02 gauss-seidel spectral radius is 0.9985249 estimated iterations to convergence 206 setup time was (sec) 0.8400000 now iterating at: 08:25:27 rms-change max change #iterations 4.141171 164.1893 at 10iterations 1.879508 66.06667 at 20iterations 0.8546765 30.18056 at 30iterations 0.3913446 11.95312 at 40iterations 0.1775704 5.468018 at 50iterations 8.1021458E-02 2.655287 at 60iterations 3.6914211E-02 1.264668 at 70iterations 1.6796235E-02 0.5477524 at 80iterations 7.6536858E-03 0.2397156 at 90iterations 3.4860631E-03 0.1059964 at 100iterations 1.5930177E-03 5.0211906E-02 at 110iterations 7.2555710E-04 2.4068832E-02 at 120iterations finished qdiffx linear iterations at : 08:25:34 total time elapsed so far: 7.370000 # loops : 120 mean,max change (kT/e) : 7.2555710E-04 2.4068832E-02 energy calculations done at 7.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.570000 DelPhi exited at 08:25:35 7.575u 0.142s 0:08.13 94.8% 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 Tue Oct 11 2011 at 08:25:35 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3195 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.720141 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): -11.60800 37.14800 ymin,ymax (A): -27.25600 21.31700 zmin,zma (A): -13.19500 45.69900 x,y,z range (A): 48.75600 48.57300 58.89400 scale (grids/A): 2.720141 object centre (A): 12.77000 -2.969501 16.25200 number of atom coordinates read : 3195 total number of charged atoms : 2779 net assigned charge : -0.8599826 assigned positive charge : 444.4134 centred at (gu) : 90.73820 94.39702 100.1989 assigned negative charge : -445.2742 centred at (gu) : 89.96906 93.96796 99.66768 start vw surface at 0.1600000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 176685 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24188 grid for indexing accessible points = 1.400000 m= 88850 mr = 130552 m= 29859 mr = 73180 m= 6420 mr = 23983 m= 757 mr = 4764 m= 26 mr = 440 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 9966 time to turn everything in is 1.380000 number of dielectric boundary points 69674 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 22229 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) : 1.813427 object centre at (A) : 12.77000 -2.969501 16.25200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.010600 0.2804933 midg,1,midg; midg,igrid,midg -0.1022087 1.9802358E-02 1,midg,midg; igrid,midg,midg -5.8760732E-02 0.3690507 gauss-seidel spectral radius is 0.9992267 estimated iterations to convergence 284 setup time was (sec) 1.680000 now iterating at: 08:25:36 rms-change max change #iterations 9.947551 387.0327 at 10iterations 5.760026 150.2951 at 20iterations 3.313969 81.37497 at 30iterations 1.901718 38.62873 at 40iterations 1.089592 21.10502 at 50iterations 0.6211964 11.71405 at 60iterations 0.3561525 6.620434 at 70iterations 0.2026400 4.162687 at 80iterations 0.1153039 2.098694 at 90iterations 6.5569669E-02 1.168526 at 100iterations 3.7410442E-02 0.7164812 at 110iterations 2.1293227E-02 0.4045112 at 120iterations 1.2090929E-02 0.2100182 at 130iterations 6.8989382E-03 0.1275141 at 140iterations 3.9322274E-03 7.0524216E-02 at 150iterations 2.2479182E-03 4.4666767E-02 at 160iterations 1.2902868E-03 2.2293091E-02 at 170iterations 7.4563752E-04 1.3950825E-02 at 180iterations finished qdiffx linear iterations at : 08:25:47 total time elapsed so far: 11.82000 # loops : 180 mean,max change (kT/e) : 7.4563752E-04 1.3950825E-02 energy calculations done at 11.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.01000 DelPhi exited at 08:25:47 12.008u 0.186s 0:12.57 96.8% 0+0k 0+0io 0pf+0w