Sat Oct 15 13:25:39 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 15 2011 at 13:25:39 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1943 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5576004 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): -35.25300 12.43200 ymin,ymax (A): -0.9800000 42.18100 zmin,zma (A): -2.407000 61.43800 x,y,z range (A): 47.68500 43.16100 63.84500 scale (grids/A): 0.5576004 object centre (A): -11.41050 20.60050 29.51550 number of atom coordinates read : 1943 total number of charged atoms : 1813 net assigned charge : 5.000010 assigned positive charge : 286.3641 centred at (gu) : 89.73679 90.02895 89.23587 assigned negative charge : -281.3644 centred at (gu) : 89.65424 90.18177 89.20528 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4122 nv = 96 ne = 84 npr = 38283 no. pairs analyzed = 38283 no. exposed pairs = 2484 no. arc points = 17910 no. surface atoms = 848 nbur = 1095 mkacc time = 7.0000000E-02 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 = 1.540000 m= 178 mr = 2124 m= 0 mr = 7 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1500000 number of dielectric boundary points 2169 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1867 ## 245 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 5193 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4903699E-10 5.7286392E-10 midg,1,midg; midg,igrid,midg 1.4458804E-09 -5.1553661E-10 1,midg,midg; igrid,midg,midg -5.0751490E-11 9.5425123E-10 gauss-seidel spectral radius is 0.9833330 estimated iterations to convergence 64 setup time was (sec) 0.3500000 now iterating at: 13:25:40 rms-change max change #iterations 6.4767145E-02 15.11956 at 10iterations 4.5937817E-03 0.8191285 at 20iterations 3.1990255E-04 6.0398102E-02 at 30iterations 2.1963620E-05 4.0340424E-03 at 40iterations 1.5590699E-06 3.0517578E-04 at 50iterations finished qdiffx linear iterations at : 13:25:46 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 1.5590699E-06 3.0517578E-04 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 13:25:46 3.540u 0.207s 0:06.92 54.0% 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 15 2011 at 13:25:46 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1943 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.672801 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): -35.25300 12.43200 ymin,ymax (A): -0.9800000 42.18100 zmin,zma (A): -2.407000 61.43800 x,y,z range (A): 47.68500 43.16100 63.84500 scale (grids/A): 1.672801 object centre (A): -11.41050 20.60050 29.51550 number of atom coordinates read : 1943 total number of charged atoms : 1813 net assigned charge : 5.000010 assigned positive charge : 286.3641 centred at (gu) : 89.21047 90.08686 87.70757 assigned negative charge : -281.3644 centred at (gu) : 88.96300 90.54572 87.61606 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 44992 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17910 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 15121 mr = 30018 m= 1879 mr = 10929 m= 62 mr = 1035 m= 0 mr = 4 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 222 time to turn everything in is 0.2600000 number of dielectric boundary points 20068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 197 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 13999 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) : 0.5576004 object centre at (A) : -11.41050 20.60050 29.51550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0340595E-02 2.0091889E-02 midg,1,midg; midg,igrid,midg 6.0598934E-03 -4.7889310E-03 1,midg,midg; igrid,midg,midg -8.2579313E-04 1.2248588E-03 gauss-seidel spectral radius is 0.9981583 estimated iterations to convergence 185 setup time was (sec) 0.5100000 now iterating at: 13:25:47 rms-change max change #iterations 2.737203 168.9981 at 10iterations 1.125111 52.38014 at 20iterations 0.4641888 20.88323 at 30iterations 0.1924464 7.831024 at 40iterations 7.9438232E-02 3.603042 at 50iterations 3.3122741E-02 1.395565 at 60iterations 1.3716869E-02 0.6075382 at 70iterations 5.6501455E-03 0.2602248 at 80iterations 2.3301651E-03 0.1066170 at 90iterations 9.7496959E-04 3.8745880E-02 at 100iterations 4.0212268E-04 1.8569946E-02 at 110iterations 1.6674775E-04 7.2517395E-03 at 120iterations finished qdiffx linear iterations at : 13:25:54 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 1.6674775E-04 7.2517395E-03 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 13:25:55 7.940u 0.211s 0:08.41 96.9% 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 Sat Oct 15 2011 at 13:25:55 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1943 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.509202 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): -35.25300 12.43200 ymin,ymax (A): -0.9800000 42.18100 zmin,zma (A): -2.407000 61.43800 x,y,z range (A): 47.68500 43.16100 63.84500 scale (grids/A): 2.509202 object centre (A): -11.41050 20.60050 29.51550 number of atom coordinates read : 1943 total number of charged atoms : 1813 net assigned charge : 5.000010 assigned positive charge : 286.3641 centred at (gu) : 88.81577 90.13037 86.56123 assigned negative charge : -281.3644 centred at (gu) : 88.44444 90.81853 86.42401 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 104216 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17910 grid for indexing accessible points = 1.400000 m= 50519 mr = 73160 m= 16376 mr = 40712 m= 3042 mr = 13030 m= 268 mr = 2109 m= 4 mr = 129 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 750 time to turn everything in is 0.5800000 number of dielectric boundary points 45285 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 14494 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) : 1.672801 object centre at (A) : -11.41050 20.60050 29.51550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2619139 0.2079579 midg,1,midg; midg,igrid,midg 6.4780563E-02 -7.9172440E-02 1,midg,midg; igrid,midg,midg -2.7766688E-02 1.6253209E-02 gauss-seidel spectral radius is 0.9990981 estimated iterations to convergence 263 setup time was (sec) 0.8100000 now iterating at: 13:25:56 rms-change max change #iterations 6.819942 352.4297 at 10iterations 3.717933 99.90607 at 20iterations 2.015814 51.08784 at 30iterations 1.093104 26.07374 at 40iterations 0.5924735 14.83380 at 50iterations 0.3216138 8.283887 at 60iterations 0.1741312 4.018265 at 70iterations 9.4240896E-02 2.204912 at 80iterations 5.0855357E-02 1.222519 at 90iterations 2.7561724E-02 0.7199736 at 100iterations 1.4877088E-02 0.3520012 at 110iterations 8.0767069E-03 0.1956139 at 120iterations 4.3514357E-03 0.1009841 at 130iterations 2.3577742E-03 5.7867289E-02 at 140iterations 1.2732990E-03 3.3170700E-02 at 150iterations 6.8797410E-04 1.5467167E-02 at 160iterations 3.7180065E-04 9.7217560E-03 at 170iterations 2.0104070E-04 4.9018860E-03 at 180iterations finished qdiffx linear iterations at : 13:26:07 total time elapsed so far: 12.13000 # loops : 180 mean,max change (kT/e) : 2.0104070E-04 4.9018860E-03 energy calculations done at 12.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.26000 DelPhi exited at 13:26:08 12.260u 0.214s 0:12.98 96.0% 0+0k 0+0io 0pf+0w