Sun Oct 9 09:35:51 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 09:35:51 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2730 !!! WARNING: GLN 1020 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5718141 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): -80.78800 -33.18500 ymin,ymax (A): -35.55800 26.70000 zmin,zma (A): -51.76900 8.035000 x,y,z range (A): 47.60300 62.25800 59.80400 scale (grids/A): 0.5718141 object centre (A): -56.98650 -4.429000 -21.86700 number of atom coordinates read : 2730 total number of charged atoms : 2586 net assigned charge : 0.7280180 assigned positive charge : 405.5566 centred at (gu) : 89.56196 89.14242 87.93913 assigned negative charge : -404.8295 centred at (gu) : 89.58928 89.36007 87.98705 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6012 nv = 96 ne = 84 npr = 53118 no. pairs analyzed = 53118 no. exposed pairs = 3828 no. arc points = 27116 no. surface atoms = 1275 nbur = 1455 mkacc time = 9.0000004E-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 = 1.512000 m= 291 mr = 2961 m= 0 mr = 7 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3335 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2713 ## 304 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7636 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3087742E-09 -4.0058673E-10 midg,1,midg; midg,igrid,midg 4.0407779E-09 -2.6941156E-09 1,midg,midg; igrid,midg,midg 5.3797072E-10 -3.0820296E-10 gauss-seidel spectral radius is 0.9842082 estimated iterations to convergence 65 setup time was (sec) 0.4000000 now iterating at: 09:35:51 rms-change max change #iterations 8.6737290E-02 14.24616 at 10iterations 6.5579279E-03 1.095783 at 20iterations 5.0228764E-04 8.6547852E-02 at 30iterations 4.2267213E-05 7.2402954E-03 at 40iterations 6.7185379E-06 1.6518831E-03 at 50iterations finished qdiffx linear iterations at : 09:35:54 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 6.7185379E-06 1.6518831E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 09:35:55 3.552u 0.201s 0:04.03 93.0% 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 Sun Oct 9 2011 at 09:35:55 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2730 !!! WARNING: GLN 1020 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.715442 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): -80.78800 -33.18500 ymin,ymax (A): -35.55800 26.70000 zmin,zma (A): -51.76900 8.035000 x,y,z range (A): 47.60300 62.25800 59.80400 scale (grids/A): 1.715442 object centre (A): -56.98650 -4.429000 -21.86700 number of atom coordinates read : 2730 total number of charged atoms : 2586 net assigned charge : 0.7280180 assigned positive charge : 405.5566 centred at (gu) : 88.68506 87.42677 83.81683 assigned negative charge : -404.8295 centred at (gu) : 88.76768 88.07992 83.96096 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 65494 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27116 grid for indexing accessible points = 1.400000 m= 21188 mr = 42743 m= 2642 mr = 14471 m= 124 mr = 1324 m= 5 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 126 time to turn everything in is 0.3400000 number of dielectric boundary points 30891 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 248 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 20050 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) : 0.5718141 object centre at (A) : -56.98650 -4.429000 -21.86700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9842924E-03 2.0500128E-03 midg,1,midg; midg,igrid,midg 8.7166950E-03 -1.4302160E-02 1,midg,midg; igrid,midg,midg 8.3680041E-03 3.0976597E-03 gauss-seidel spectral radius is 0.9983453 estimated iterations to convergence 195 setup time was (sec) 0.5600000 now iterating at: 09:35:56 rms-change max change #iterations 3.535445 203.0540 at 10iterations 1.520306 55.93909 at 20iterations 0.6570786 25.45314 at 30iterations 0.2838143 9.826157 at 40iterations 0.1230446 4.526786 at 50iterations 5.3200733E-02 1.950775 at 60iterations 2.3072755E-02 0.8940964 at 70iterations 9.9496003E-03 0.3518577 at 80iterations 4.3411786E-03 0.1642189 at 90iterations 1.8788197E-03 6.2493324E-02 at 100iterations 8.1463601E-04 2.7839661E-02 at 110iterations 3.5333011E-04 1.2769699E-02 at 120iterations finished qdiffx linear iterations at : 09:36:03 total time elapsed so far: 8.010000 # loops : 120 mean,max change (kT/e) : 3.5333011E-04 1.2769699E-02 energy calculations done at 8.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.140000 DelPhi exited at 09:36:04 8.147u 0.223s 0:08.64 96.7% 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 09:36:04 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2730 !!! WARNING: GLN 1020 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.573164 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): -80.78800 -33.18500 ymin,ymax (A): -35.55800 26.70000 zmin,zma (A): -51.76900 8.035000 x,y,z range (A): 47.60300 62.25800 59.80400 scale (grids/A): 2.573164 object centre (A): -56.98650 -4.429000 -21.86700 number of atom coordinates read : 2730 total number of charged atoms : 2586 net assigned charge : 0.7280180 assigned positive charge : 405.5566 centred at (gu) : 88.02728 86.13996 80.72492 assigned negative charge : -404.8295 centred at (gu) : 88.15146 87.11989 80.94139 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 151552 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27116 grid for indexing accessible points = 1.400000 m= 70766 mr = 104580 m= 22673 mr = 55238 m= 4289 mr = 17081 m= 482 mr = 2844 m= 9 mr = 233 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 504 time to turn everything in is 0.8400000 number of dielectric boundary points 69795 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 20679 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) : 1.715442 object centre at (A) : -56.98650 -4.429000 -21.86700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.7149644E-02 -1.0289554E-02 midg,1,midg; midg,igrid,midg 0.2285218 0.1662092 1,midg,midg; igrid,midg,midg 0.1271768 6.5560199E-02 gauss-seidel spectral radius is 0.9991870 estimated iterations to convergence 277 setup time was (sec) 1.080000 now iterating at: 09:36:05 rms-change max change #iterations 8.916968 289.6788 at 10iterations 5.121021 125.5219 at 20iterations 2.909238 66.93165 at 30iterations 1.647642 38.43398 at 40iterations 0.9304727 20.68216 at 50iterations 0.5230001 10.79659 at 60iterations 0.2942443 6.138721 at 70iterations 0.1653149 3.664186 at 80iterations 9.2383921E-02 1.844843 at 90iterations 5.1857237E-02 1.105268 at 100iterations 2.9048858E-02 0.5793753 at 110iterations 1.6262716E-02 0.3068485 at 120iterations 9.1378847E-03 0.1803436 at 130iterations 5.1240968E-03 9.8839760E-02 at 140iterations 2.8836592E-03 5.6547165E-02 at 150iterations 1.6348020E-03 3.8120270E-02 at 160iterations 9.3836314E-04 2.4321079E-02 at 170iterations 5.5125268E-04 1.3805389E-02 at 180iterations finished qdiffx linear iterations at : 09:36:17 total time elapsed so far: 12.90000 # loops : 180 mean,max change (kT/e) : 5.5125268E-04 1.3805389E-02 energy calculations done at 12.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.03000 DelPhi exited at 09:36:17 13.033u 0.228s 0:13.56 97.7% 0+0k 0+0io 0pf+0w