Mon Oct 10 09:44:29 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 Mon Oct 10 2011 at 09:44:29 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2912 !!! WARNING: HIT 231 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6030423 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): -17.85000 34.01500 ymin,ymax (A): -60.01800 -0.9840001 zmin,zma (A): -0.5770000 57.92300 x,y,z range (A): 51.86500 59.03400 58.50000 scale (grids/A): 0.6030423 object centre (A): 8.082500 -30.50100 28.67300 number of atom coordinates read : 2912 total number of charged atoms : 2759 net assigned charge : 7.014013 assigned positive charge : 427.7137 centred at (gu) : 89.01032 88.20352 88.02083 assigned negative charge : -420.7003 centred at (gu) : 89.15914 88.04148 87.92781 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7232 nv = 96 ne = 84 npr = 55702 no. pairs analyzed = 55702 no. exposed pairs = 4456 no. arc points = 32325 no. surface atoms = 1477 nbur = 1435 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 398 mr = 3190 m= 3 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4411 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3069 ## 316 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8819 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0515442E-09 4.7758211E-09 midg,1,midg; midg,igrid,midg -5.6412950E-09 6.8871535E-09 1,midg,midg; igrid,midg,midg 1.2206869E-08 -2.4014144E-09 gauss-seidel spectral radius is 0.9858164 estimated iterations to convergence 69 setup time was (sec) 0.5700000 now iterating at: 09:44:30 rms-change max change #iterations 0.1146582 18.97825 at 10iterations 9.3904724E-03 1.435987 at 20iterations 8.4220472E-04 0.1355095 at 30iterations 7.6617594E-05 1.2106895E-02 at 40iterations 1.0297899E-05 1.4266968E-03 at 50iterations finished qdiffx linear iterations at : 09:44:32 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 1.0297899E-05 1.4266968E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 09:44:33 3.506u 0.201s 0:04.41 83.9% 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 Mon Oct 10 2011 at 09:44:33 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2912 !!! WARNING: HIT 231 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.809127 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): -17.85000 34.01500 ymin,ymax (A): -60.01800 -0.9840001 zmin,zma (A): -0.5770000 57.92300 x,y,z range (A): 51.86500 59.03400 58.50000 scale (grids/A): 1.809127 object centre (A): 8.082500 -30.50100 28.67300 number of atom coordinates read : 2912 total number of charged atoms : 2759 net assigned charge : 7.014013 assigned positive charge : 427.7137 centred at (gu) : 87.03032 84.60992 84.06174 assigned negative charge : -420.7003 centred at (gu) : 87.47723 84.12410 83.78320 start vw surface at 0.2000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 76978 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32325 grid for indexing accessible points = 1.400000 m= 25314 mr = 46911 m= 3769 mr = 16400 m= 183 mr = 1851 m= 4 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 41048 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 235 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 21531 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) : 0.6030423 object centre at (A) : 8.082500 -30.50100 28.67300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4136297E-02 4.3264786E-03 midg,1,midg; midg,igrid,midg 2.8048117E-02 4.1422043E-02 1,midg,midg; igrid,midg,midg 1.4054763E-02 8.9113554E-03 gauss-seidel spectral radius is 0.9985489 estimated iterations to convergence 208 setup time was (sec) 0.9100000 now iterating at: 09:44:34 rms-change max change #iterations 4.042156 182.9022 at 10iterations 1.846987 67.52757 at 20iterations 0.8450446 28.39134 at 30iterations 0.3855458 14.74428 at 40iterations 0.1755337 5.833702 at 50iterations 8.0030076E-02 2.595048 at 60iterations 3.6757179E-02 1.294997 at 70iterations 1.6720505E-02 0.5450974 at 80iterations 7.6734633E-03 0.2706581 at 90iterations 3.4928892E-03 0.1144047 at 100iterations 1.6025873E-03 5.5689812E-02 at 110iterations 7.3127385E-04 2.2159576E-02 at 120iterations finished qdiffx linear iterations at : 09:44:41 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 7.3127385E-04 2.2159576E-02 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 09:44:42 7.806u 0.228s 0:09.05 88.6% 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 09:44:42 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2912 !!! WARNING: HIT 231 has a net charge of 0.5140 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: 2.713690 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): -17.85000 34.01500 ymin,ymax (A): -60.01800 -0.9840001 zmin,zma (A): -0.5770000 57.92300 x,y,z range (A): 51.86500 59.03400 58.50000 scale (grids/A): 2.713690 object centre (A): 8.082500 -30.50100 28.67300 number of atom coordinates read : 2912 total number of charged atoms : 2759 net assigned charge : 7.014013 assigned positive charge : 427.7137 centred at (gu) : 85.54539 81.91476 81.09259 assigned negative charge : -420.7003 centred at (gu) : 86.21577 81.18606 80.67477 start vw surface at 0.1600000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 177690 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32325 grid for indexing accessible points = 1.400000 m= 81510 mr = 115952 m= 28264 mr = 61194 m= 6368 mr = 20584 m= 771 mr = 4093 m= 49 mr = 396 m= 2 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.8700001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.480000 number of dielectric boundary points 92428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 22069 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) : 1.809127 object centre at (A) : 8.082500 -30.50100 28.67300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1097421 4.2494684E-02 midg,1,midg; midg,igrid,midg 0.4984615 0.5105491 1,midg,midg; igrid,midg,midg 4.5599185E-02 0.1248439 gauss-seidel spectral radius is 0.9992728 estimated iterations to convergence 293 setup time was (sec) 1.800000 now iterating at: 09:44:44 rms-change max change #iterations 10.12400 392.8629 at 10iterations 6.136285 180.6501 at 20iterations 3.658646 104.5369 at 30iterations 2.168059 50.56295 at 40iterations 1.274841 28.53594 at 50iterations 0.7492714 16.27569 at 60iterations 0.4378835 9.427282 at 70iterations 0.2549573 5.703910 at 80iterations 0.1488215 3.662441 at 90iterations 8.6371355E-02 1.846595 at 100iterations 5.0205696E-02 1.117022 at 110iterations 2.9088929E-02 0.5750821 at 120iterations 1.6885972E-02 0.3268535 at 130iterations 9.7717261E-03 0.1902423 at 140iterations 5.6557967E-03 0.1196022 at 150iterations 3.2746200E-03 5.9933186E-02 at 160iterations 1.8946205E-03 4.0331751E-02 at 170iterations 1.0957273E-03 2.0591736E-02 at 180iterations finished qdiffx linear iterations at : 09:44:56 total time elapsed so far: 13.08000 # loops : 180 mean,max change (kT/e) : 1.0957273E-03 2.0591736E-02 energy calculations done at 13.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.26000 DelPhi exited at 09:44:56 13.263u 0.222s 0:13.82 97.5% 0+0k 0+0io 0pf+0w