Mon Oct 10 10:40:42 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 Mon Oct 10 2011 at 10:40:43 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 = 5014 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5406473 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): 3.751000 62.98700 ymin,ymax (A): -24.19900 37.85400 zmin,zma (A): -33.44000 32.40700 x,y,z range (A): 59.23600 62.05300 65.84700 scale (grids/A): 0.5406473 object centre (A): 33.36900 6.827500 -0.5165024 number of atom coordinates read : 5014 total number of charged atoms : 4814 net assigned charge : 8.500036 assigned positive charge : 777.8674 centred at (gu) : 89.76656 90.85563 88.64484 assigned negative charge : -769.3746 centred at (gu) : 89.79533 90.89427 88.64254 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 9438 nv = 96 ne = 84 npr = 100668 no. pairs analyzed = 100668 no. exposed pairs = 5767 no. arc points = 38715 no. surface atoms = 1934 nbur = 3080 mkacc time = 0.2600000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 363 mr = 5452 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 145 time to turn everything in is 0.5200000 number of dielectric boundary points 4338 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3953 ## 519 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 12417 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.6889349E-10 3.2596403E-10 midg,1,midg; midg,igrid,midg 6.4057532E-10 7.7008934E-11 1,midg,midg; igrid,midg,midg 7.4071410E-10 1.5153435E-10 gauss-seidel spectral radius is 0.9825084 estimated iterations to convergence 62 setup time was (sec) 0.8000000 now iterating at: 10:40:44 rms-change max change #iterations 9.5656790E-02 12.24889 at 10iterations 6.5660188E-03 0.8634186 at 20iterations 8.8147545E-04 0.1221161 at 30iterations 3.9831863E-04 5.3599358E-02 at 40iterations 2.0493634E-04 2.7707100E-02 at 50iterations finished qdiffx linear iterations at : 10:40:47 total time elapsed so far: 4.520000 # loops : 50 mean,max change (kT/e) : 2.0493634E-04 2.7707100E-02 energy calculations done at 4.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.690000 DelPhi exited at 10:40:48 4.699u 0.429s 0:05.47 93.4% 0+0k 0+0io 6pf+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 10:40:48 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 = 5014 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.621942 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): 3.751000 62.98700 ymin,ymax (A): -24.19900 37.85400 zmin,zma (A): -33.44000 32.40700 x,y,z range (A): 59.23600 62.05300 65.84700 scale (grids/A): 1.621942 object centre (A): 33.36900 6.827500 -0.5165024 number of atom coordinates read : 5014 total number of charged atoms : 4814 net assigned charge : 8.500036 assigned positive charge : 777.8674 centred at (gu) : 89.29742 92.56490 85.93277 assigned negative charge : -769.3746 centred at (gu) : 89.38597 92.68276 85.92780 start vw surface at 0.1800000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 107446 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38715 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 35226 mr = 78536 m= 3570 mr = 25632 m= 93 mr = 1821 m= 0 mr = 7 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 5535 time to turn everything in is 0.8400000 number of dielectric boundary points 40339 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 409 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 36729 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) : 0.5406473 object centre at (A) : 33.36900 6.827500 -0.5165024 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5443995E-02 6.3845380E-03 midg,1,midg; midg,igrid,midg 2.4963116E-02 1.1219014E-02 1,midg,midg; igrid,midg,midg -3.1397995E-03 -6.0169394E-03 gauss-seidel spectral radius is 0.9983501 estimated iterations to convergence 195 setup time was (sec) 1.160000 now iterating at: 10:40:50 rms-change max change #iterations 4.513903 158.0081 at 10iterations 1.955359 57.76589 at 20iterations 0.8532600 26.74307 at 30iterations 0.3723315 10.54137 at 40iterations 0.1621615 4.778175 at 50iterations 7.0659027E-02 1.973074 at 60iterations 3.0836763E-02 0.8947182 at 70iterations 1.3545158E-02 0.3870316 at 80iterations 6.0244934E-03 0.1669197 at 90iterations 2.8055867E-03 8.3335876E-02 at 100iterations 1.4464196E-03 4.6916962E-02 at 110iterations 8.8219653E-04 2.8196335E-02 at 120iterations finished qdiffx linear iterations at : 10:40:59 total time elapsed so far: 10.79000 # loops : 120 mean,max change (kT/e) : 8.8219653E-04 2.8196335E-02 energy calculations done at 10.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.96000 DelPhi exited at 10:41:00 10.965u 0.453s 0:11.80 96.6% 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 10:41:00 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 = 5014 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.432913 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): 3.751000 62.98700 ymin,ymax (A): -24.19900 37.85400 zmin,zma (A): -33.44000 32.40700 x,y,z range (A): 59.23600 62.05300 65.84700 scale (grids/A): 2.432913 object centre (A): 33.36900 6.827500 -0.5165024 number of atom coordinates read : 5014 total number of charged atoms : 4814 net assigned charge : 8.500036 assigned positive charge : 777.8674 centred at (gu) : 88.94577 93.84687 83.89885 assigned negative charge : -769.3746 centred at (gu) : 89.07888 94.02416 83.89176 start vw surface at 0.1700000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 250197 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38715 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 122568 mr = 191136 m= 35365 mr = 100534 m= 5573 mr = 27399 m= 340 mr = 3750 m= 7 mr = 154 m= 0 mr = 0 time to grow re-entrant surface = 1.340000 no. cavity mid-points inaccessible to solvent = 18492 time to turn everything in is 2.130000 number of dielectric boundary points 91077 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 2.290000 number of grid points assigned charge 38457 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) : 1.621942 object centre at (A) : 33.36900 6.827500 -0.5165024 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4896418 7.3079765E-02 midg,1,midg; midg,igrid,midg 0.5293886 9.4585977E-02 1,midg,midg; igrid,midg,midg -9.8115563E-02 4.8258025E-03 gauss-seidel spectral radius is 0.9992214 estimated iterations to convergence 283 setup time was (sec) 2.500000 now iterating at: 10:41:03 rms-change max change #iterations 11.51864 266.1931 at 10iterations 6.666377 143.8638 at 20iterations 3.846720 89.29985 at 30iterations 2.211164 47.63428 at 40iterations 1.267575 23.68012 at 50iterations 0.7234101 13.48657 at 60iterations 0.4136040 6.813861 at 70iterations 0.2352629 3.892144 at 80iterations 0.1339288 2.398254 at 90iterations 7.6220952E-02 1.270416 at 100iterations 4.3389522E-02 0.7358360 at 110iterations 2.4647165E-02 0.4248276 at 120iterations 1.3988304E-02 0.2402687 at 130iterations 7.9509355E-03 0.1330729 at 140iterations 4.5126122E-03 7.8857422E-02 at 150iterations 2.5680512E-03 4.2971611E-02 at 160iterations 1.4672485E-03 2.7982712E-02 at 170iterations 8.4288471E-04 1.5096664E-02 at 180iterations finished qdiffx linear iterations at : 10:41:21 total time elapsed so far: 20.78000 # loops : 180 mean,max change (kT/e) : 8.4288471E-04 1.5096664E-02 energy calculations done at 20.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.94000 DelPhi exited at 10:41:22 20.941u 0.507s 0:21.76 98.5% 0+0k 0+0io 0pf+0w