Tue Oct 11 07:51:42 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+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 Tue Oct 11 2011 at 07:51:42 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2374 !!! WARNING: HIR 45 has a net charge of 0.5140 !!! WARNING: HIR 93 has a net charge of 0.5140 !!! WARNING: SEP 192 has a net charge of -0.4750 !!! WARNING: GLM 194 has a net charge of -0.0940 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: 0.6418115 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): -9.044000 36.56100 ymin,ymax (A): -14.63700 40.83100 zmin,zma (A): 5.167000 52.62900 x,y,z range (A): 45.60500 55.46800 47.46200 scale (grids/A): 0.6418115 object centre (A): 13.75850 13.09700 28.89800 number of atom coordinates read : 2374 total number of charged atoms : 2232 net assigned charge : 3.959008 assigned positive charge : 358.1674 centred at (gu) : 90.52575 88.73531 90.67706 assigned negative charge : -354.2088 centred at (gu) : 90.44019 88.74719 90.82993 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6476 nv = 96 ne = 84 npr = 48211 no. pairs analyzed = 48211 no. exposed pairs = 2853 no. arc points = 19885 no. surface atoms = 980 nbur = 1394 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 357 mr = 3602 m= 2 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3176 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2066 ## 205 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7849 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9823009E-08 -1.3063621E-08 midg,1,midg; midg,igrid,midg 9.7186117E-09 3.7232508E-09 1,midg,midg; igrid,midg,midg -3.0941234E-09 1.7443890E-08 gauss-seidel spectral radius is 0.9873989 estimated iterations to convergence 73 setup time was (sec) 0.3600000 now iterating at: 07:51:43 rms-change max change #iterations 0.1446445 21.57639 at 10iterations 1.5029695E-02 2.213397 at 20iterations 1.7376014E-03 0.2855148 at 30iterations 2.7559919E-04 4.2301178E-02 at 40iterations 6.0266997E-05 9.5329285E-03 at 50iterations finished qdiffx linear iterations at : 07:51:45 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 6.0266997E-05 9.5329285E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 07:51:46 3.323u 0.178s 0:04.29 81.3% 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 Tue Oct 11 2011 at 07:51:46 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2374 !!! WARNING: HIR 45 has a net charge of 0.5140 !!! WARNING: HIR 93 has a net charge of 0.5140 !!! WARNING: SEP 192 has a net charge of -0.4750 !!! WARNING: GLM 194 has a net charge of -0.0940 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: 1.925434 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): -9.044000 36.56100 ymin,ymax (A): -14.63700 40.83100 zmin,zma (A): 5.167000 52.62900 x,y,z range (A): 45.60500 55.46800 47.46200 scale (grids/A): 1.925434 object centre (A): 13.75850 13.09700 28.89800 number of atom coordinates read : 2374 total number of charged atoms : 2232 net assigned charge : 3.959008 assigned positive charge : 358.1674 centred at (gu) : 91.57706 86.20558 92.03078 assigned negative charge : -354.2088 centred at (gu) : 91.32043 86.24151 92.48971 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69242 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19885 grid for indexing accessible points = 1.400000 m= 26785 mr = 48216 m= 4691 mr = 20140 m= 318 mr = 3104 m= 7 mr = 126 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 299 time to turn everything in is 0.3500000 number of dielectric boundary points 29457 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 17551 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) : 0.6418115 object centre at (A) : 13.75850 13.09700 28.89800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6989111E-02 -2.4051219E-02 midg,1,midg; midg,igrid,midg 1.9627202E-02 3.2406598E-02 1,midg,midg; igrid,midg,midg -5.4910737E-03 6.3256179E-03 gauss-seidel spectral radius is 0.9986373 estimated iterations to convergence 215 setup time was (sec) 0.5600000 now iterating at: 07:51:47 rms-change max change #iterations 4.111341 206.9176 at 10iterations 1.929125 66.70650 at 20iterations 0.9111401 29.64937 at 30iterations 0.4247810 13.56606 at 40iterations 0.2011576 7.664779 at 50iterations 9.4398573E-02 3.123935 at 60iterations 4.4465184E-02 1.464606 at 70iterations 2.0892978E-02 0.6965141 at 80iterations 9.8541677E-03 0.3288078 at 90iterations 4.6957619E-03 0.1675014 at 100iterations 2.2396459E-03 7.8137517E-02 at 110iterations 1.0821030E-03 3.7200928E-02 at 120iterations finished qdiffx linear iterations at : 07:51:54 total time elapsed so far: 7.530000 # loops : 120 mean,max change (kT/e) : 1.0821030E-03 3.7200928E-02 energy calculations done at 7.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 07:51:55 7.671u 0.190s 0:08.46 92.9% 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 07:51:55 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2374 !!! WARNING: HIR 45 has a net charge of 0.5140 !!! WARNING: HIR 93 has a net charge of 0.5140 !!! WARNING: SEP 192 has a net charge of -0.4750 !!! WARNING: GLM 194 has a net charge of -0.0940 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: 2.888152 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): -9.044000 36.56100 ymin,ymax (A): -14.63700 40.83100 zmin,zma (A): 5.167000 52.62900 x,y,z range (A): 45.60500 55.46800 47.46200 scale (grids/A): 2.888152 object centre (A): 13.75850 13.09700 28.89800 number of atom coordinates read : 2374 total number of charged atoms : 2232 net assigned charge : 3.959008 assigned positive charge : 358.1674 centred at (gu) : 92.36547 84.30833 93.04618 assigned negative charge : -354.2088 centred at (gu) : 91.98064 84.36224 93.73453 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 159664 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19885 grid for indexing accessible points = 1.400000 m= 84324 mr = 116262 m= 33035 mr = 69727 m= 8551 mr = 27067 m= 1313 mr = 6581 m= 83 mr = 924 m= 4 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 1092 time to turn everything in is 0.9100000 number of dielectric boundary points 66365 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 17844 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) : 1.925434 object centre at (A) : 13.75850 13.09700 28.89800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4191120 -0.3328768 midg,1,midg; midg,igrid,midg 0.1328205 0.3202592 1,midg,midg; igrid,midg,midg -3.5045635E-02 -3.9242073E-03 gauss-seidel spectral radius is 0.9992497 estimated iterations to convergence 288 setup time was (sec) 1.130000 now iterating at: 07:51:56 rms-change max change #iterations 9.596807 410.2984 at 10iterations 5.593351 128.3834 at 20iterations 3.245283 89.42468 at 30iterations 1.875032 34.98379 at 40iterations 1.081486 21.97746 at 50iterations 0.6228159 11.10701 at 60iterations 0.3584510 6.768706 at 70iterations 0.2057258 3.937078 at 80iterations 0.1182190 2.154615 at 90iterations 6.7641042E-02 1.177172 at 100iterations 3.8725551E-02 0.7477226 at 110iterations 2.2249946E-02 0.4141579 at 120iterations 1.2739435E-02 0.2535629 at 130iterations 7.3162271E-03 0.1534996 at 140iterations 4.1906922E-03 7.8367233E-02 at 150iterations 2.4078365E-03 4.5917511E-02 at 160iterations 1.3850793E-03 2.6412129E-02 at 170iterations 8.0014224E-04 1.5472412E-02 at 180iterations finished qdiffx linear iterations at : 07:52:07 total time elapsed so far: 12.23000 # loops : 180 mean,max change (kT/e) : 8.0014224E-04 1.5472412E-02 energy calculations done at 12.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.36000 DelPhi exited at 07:52:08 12.367u 0.206s 0:13.22 95.0% 0+0k 0+0io 0pf+0w