Sun Oct 9 14:09:39 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 Sun Oct 9 2011 at 14:09:39 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: HIQ 137 has a net charge of 0.5140 !!! WARNING: VAL 225 has a net charge of -0.0260 !!! WARNING: SEP 283 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6148426 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): -13.54900 44.35200 ymin,ymax (A): -25.07700 25.64300 zmin,zma (A): 21.99700 69.74900 x,y,z range (A): 57.90100 50.72000 47.75200 scale (grids/A): 0.6148426 object centre (A): 15.40150 0.2830000 45.87300 number of atom coordinates read : 3036 total number of charged atoms : 2642 net assigned charge : 4.513018 assigned positive charge : 423.3473 centred at (gu) : 89.41473 89.24249 89.52612 assigned negative charge : -418.8354 centred at (gu) : 89.37693 89.37418 89.39957 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6984 nv = 96 ne = 84 npr = 55804 no. pairs analyzed = 55804 no. exposed pairs = 3620 no. arc points = 25123 no. surface atoms = 1211 nbur = 1825 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 389 mr = 3634 m= 0 mr = 24 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3715 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2602 ## 246 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8638 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3859890E-09 9.7099138E-09 midg,1,midg; midg,igrid,midg 1.3146156E-08 -4.3133288E-09 1,midg,midg; igrid,midg,midg 8.3899893E-10 4.7655373E-09 gauss-seidel spectral radius is 0.9863197 estimated iterations to convergence 70 setup time was (sec) 0.5200000 now iterating at: 14:09:39 rms-change max change #iterations 0.1250622 20.82405 at 10iterations 1.1454880E-02 1.945268 at 20iterations 1.1061946E-03 0.1578064 at 30iterations 1.4993167E-04 1.9546509E-02 at 40iterations 3.5001580E-05 4.5623779E-03 at 50iterations finished qdiffx linear iterations at : 14:09:42 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 3.5001580E-05 4.5623779E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 14:09:42 3.080u 0.139s 0:03.49 91.9% 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 Sun Oct 9 2011 at 14:09:42 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: HIQ 137 has a net charge of 0.5140 !!! WARNING: VAL 225 has a net charge of -0.0260 !!! WARNING: SEP 283 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.844528 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): -13.54900 44.35200 ymin,ymax (A): -25.07700 25.64300 zmin,zma (A): 21.99700 69.74900 x,y,z range (A): 57.90100 50.72000 47.75200 scale (grids/A): 1.844528 object centre (A): 15.40150 0.2830000 45.87300 number of atom coordinates read : 3036 total number of charged atoms : 2642 net assigned charge : 4.513018 assigned positive charge : 423.3473 centred at (gu) : 88.24345 87.72705 88.57778 assigned negative charge : -418.8354 centred at (gu) : 88.13072 88.12237 88.19833 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 75353 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25123 grid for indexing accessible points = 1.400000 m= 25924 mr = 51190 m= 3725 mr = 18001 m= 175 mr = 2047 m= 1 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 33902 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 194 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 20658 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) : 0.6148426 object centre at (A) : 15.40150 0.2830000 45.87300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0303361E-02 1.7022807E-02 midg,1,midg; midg,igrid,midg 2.6080422E-02 1.2277180E-02 1,midg,midg; igrid,midg,midg -4.4147395E-02 -7.2421771E-03 gauss-seidel spectral radius is 0.9985725 estimated iterations to convergence 210 setup time was (sec) 0.7900000 now iterating at: 14:09:43 rms-change max change #iterations 4.177268 208.6416 at 10iterations 1.924423 65.93321 at 20iterations 0.8845479 31.83747 at 30iterations 0.4099069 13.40177 at 40iterations 0.1880970 6.171524 at 50iterations 8.6675674E-02 2.858444 at 60iterations 3.9881181E-02 1.335627 at 70iterations 1.8452926E-02 0.5776672 at 80iterations 8.5412040E-03 0.3238716 at 90iterations 3.9680460E-03 0.1423373 at 100iterations 1.8463602E-03 6.3331604E-02 at 110iterations 8.7113457E-04 2.9017687E-02 at 120iterations finished qdiffx linear iterations at : 14:09:49 total time elapsed so far: 6.970000 # loops : 120 mean,max change (kT/e) : 8.7113457E-04 2.9017687E-02 energy calculations done at 6.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.170000 DelPhi exited at 14:09:50 7.173u 0.154s 0:07.62 96.0% 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 14:09:50 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: HIQ 137 has a net charge of 0.5140 !!! WARNING: VAL 225 has a net charge of -0.0260 !!! WARNING: SEP 283 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.766792 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): -13.54900 44.35200 ymin,ymax (A): -25.07700 25.64300 zmin,zma (A): 21.99700 69.74900 x,y,z range (A): 57.90100 50.72000 47.75200 scale (grids/A): 2.766792 object centre (A): 15.40150 0.2830000 45.87300 number of atom coordinates read : 3036 total number of charged atoms : 2642 net assigned charge : 4.513018 assigned positive charge : 423.3473 centred at (gu) : 87.36494 86.59033 87.86637 assigned negative charge : -418.8354 centred at (gu) : 87.19608 87.18351 87.29744 start vw surface at 0.1700000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 173857 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25123 grid for indexing accessible points = 1.400000 m= 85549 mr = 124310 m= 28754 mr = 67725 m= 6376 mr = 21877 m= 803 mr = 4397 m= 40 mr = 462 m= 0 mr = 12 time to grow re-entrant surface = 0.7699999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.330000 number of dielectric boundary points 76596 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 21134 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) : 1.844528 object centre at (A) : 15.40150 0.2830000 45.87300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1096114 0.1157052 midg,1,midg; midg,igrid,midg 0.2177315 0.1374377 1,midg,midg; igrid,midg,midg -0.7505459 -3.8808901E-02 gauss-seidel spectral radius is 0.9992466 estimated iterations to convergence 288 setup time was (sec) 1.610000 now iterating at: 14:09:52 rms-change max change #iterations 10.10287 374.5771 at 10iterations 5.977394 163.8450 at 20iterations 3.508351 80.25800 at 30iterations 2.039257 40.21699 at 40iterations 1.184745 23.91245 at 50iterations 0.6878714 16.75657 at 60iterations 0.3965349 7.322725 at 70iterations 0.2281714 4.468171 at 80iterations 0.1314839 2.762712 at 90iterations 7.5689711E-02 1.582591 at 100iterations 4.3456852E-02 0.8679819 at 110iterations 2.4912408E-02 0.4821777 at 120iterations 1.4319892E-02 0.2691612 at 130iterations 8.2240636E-03 0.1648216 at 140iterations 4.7354540E-03 8.4307671E-02 at 150iterations 2.7329347E-03 5.2799225E-02 at 160iterations 1.5872397E-03 3.1738281E-02 at 170iterations 9.2807744E-04 1.9813538E-02 at 180iterations finished qdiffx linear iterations at : 14:10:01 total time elapsed so far: 11.06000 # loops : 180 mean,max change (kT/e) : 9.2807744E-04 1.9813538E-02 energy calculations done at 11.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.26000 DelPhi exited at 14:10:02 11.264u 0.190s 0:11.72 97.6% 0+0k 0+0io 0pf+0w