Sun Oct 9 11:50:12 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 11:50:12 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2660 !!! WARNING: HIR 203 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6562817 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): -6.213000 47.51600 ymin,ymax (A): 8.801001 59.00000 zmin,zma (A): 5.021000 59.26600 x,y,z range (A): 53.72900 50.19900 54.24500 scale (grids/A): 0.6562817 object centre (A): 20.65150 33.90050 32.14350 number of atom coordinates read : 2660 total number of charged atoms : 2590 net assigned charge : 1.014012 assigned positive charge : 399.4230 centred at (gu) : 90.92484 90.15672 91.26656 assigned negative charge : -398.4106 centred at (gu) : 90.93824 90.15793 91.25385 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8140 nv = 96 ne = 84 npr = 50713 no. pairs analyzed = 50713 no. exposed pairs = 3691 no. arc points = 26861 no. surface atoms = 1224 nbur = 1436 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 567 mr = 4189 m= 2 mr = 101 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 0.2000000 number of dielectric boundary points 4419 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2412 ## 174 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9465 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2768621E-12 6.0623004E-09 midg,1,midg; midg,igrid,midg 2.4564157E-09 2.1583646E-09 1,midg,midg; igrid,midg,midg 3.9465506E-09 -2.2243926E-10 gauss-seidel spectral radius is 0.9879945 estimated iterations to convergence 75 setup time was (sec) 0.4000000 now iterating at: 11:50:12 rms-change max change #iterations 0.1655071 25.65498 at 10iterations 1.7501036E-02 2.461502 at 20iterations 1.8601329E-03 0.3197842 at 30iterations 2.5905218E-04 4.1313171E-02 at 40iterations 7.3360956E-05 1.3013840E-02 at 50iterations finished qdiffx linear iterations at : 11:50:15 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 7.3360956E-05 1.3013840E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 11:50:15 3.406u 0.173s 0:03.83 93.2% 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 11:50:15 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2660 !!! WARNING: HIR 203 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.968845 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): -6.213000 47.51600 ymin,ymax (A): 8.801001 59.00000 zmin,zma (A): 5.021000 59.26600 x,y,z range (A): 53.72900 50.19900 54.24500 scale (grids/A): 1.968845 object centre (A): 20.65150 33.90050 32.14350 number of atom coordinates read : 2660 total number of charged atoms : 2590 net assigned charge : 1.014012 assigned positive charge : 399.4230 centred at (gu) : 92.77371 90.46915 93.79903 assigned negative charge : -398.4106 centred at (gu) : 92.81457 90.47359 93.76137 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 86890 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26861 grid for indexing accessible points = 1.400000 m= 32835 mr = 57937 m= 6750 mr = 23518 m= 551 mr = 4463 m= 8 mr = 250 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 40866 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 20481 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) : 0.6562817 object centre at (A) : 20.65150 33.90050 32.14350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1165779E-03 2.4344707E-02 midg,1,midg; midg,igrid,midg -4.1103400E-03 3.8737312E-03 1,midg,midg; igrid,midg,midg -1.7263656E-02 -2.2254435E-03 gauss-seidel spectral radius is 0.9987563 estimated iterations to convergence 225 setup time was (sec) 0.6600000 now iterating at: 11:50:16 rms-change max change #iterations 4.615503 178.2029 at 10iterations 2.238165 64.50046 at 20iterations 1.080094 31.37963 at 30iterations 0.5229465 16.37274 at 40iterations 0.2528917 7.452713 at 50iterations 0.1220189 3.731503 at 60iterations 5.9363097E-02 1.879377 at 70iterations 2.8735975E-02 0.8591493 at 80iterations 1.3948097E-02 0.4512587 at 90iterations 6.7814323E-03 0.1928048 at 100iterations 3.3132911E-03 9.4837189E-02 at 110iterations 1.6433111E-03 4.6610117E-02 at 120iterations finished qdiffx linear iterations at : 11:50:23 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 1.6433111E-03 4.6610117E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 11:50:24 7.958u 0.201s 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 Sun Oct 9 2011 at 11:50:24 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2660 !!! WARNING: HIR 203 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.953267 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): -6.213000 47.51600 ymin,ymax (A): 8.801001 59.00000 zmin,zma (A): 5.021000 59.26600 x,y,z range (A): 53.72900 50.19900 54.24500 scale (grids/A): 2.953267 object centre (A): 20.65150 33.90050 32.14350 number of atom coordinates read : 2660 total number of charged atoms : 2590 net assigned charge : 1.014012 assigned positive charge : 399.4230 centred at (gu) : 94.16027 90.70367 95.69824 assigned negative charge : -398.4106 centred at (gu) : 94.22186 90.71029 95.64204 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 200153 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26861 grid for indexing accessible points = 1.400000 m= 101557 mr = 140669 m= 41806 mr = 81068 m= 12850 mr = 33381 m= 2507 mr = 9884 m= 219 mr = 1806 m= 4 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.120000 number of dielectric boundary points 92187 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 20719 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) : 1.968845 object centre at (A) : 20.65150 33.90050 32.14350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2368060E-02 0.3112589 midg,1,midg; midg,igrid,midg -2.3968301E-03 8.8036478E-02 1,midg,midg; igrid,midg,midg -0.2053666 0.2944296 gauss-seidel spectral radius is 0.9993138 estimated iterations to convergence 301 setup time was (sec) 1.360000 now iterating at: 11:50:25 rms-change max change #iterations 10.80944 374.6865 at 10iterations 6.529721 148.1343 at 20iterations 3.908821 77.67917 at 30iterations 2.335249 46.42858 at 40iterations 1.390238 26.66613 at 50iterations 0.8237463 16.30605 at 60iterations 0.4885083 9.240447 at 70iterations 0.2885669 4.844086 at 80iterations 0.1703498 2.897317 at 90iterations 0.1000799 1.674183 at 100iterations 5.8982894E-02 1.019711 at 110iterations 3.4708120E-02 0.6333370 at 120iterations 2.0472385E-02 0.3450933 at 130iterations 1.2055713E-02 0.2170451 at 140iterations 7.1015037E-03 0.1191216 at 150iterations 4.2029717E-03 7.1961522E-02 at 160iterations 2.4968041E-03 4.6451926E-02 at 170iterations 1.5021897E-03 2.7271271E-02 at 180iterations finished qdiffx linear iterations at : 11:50:37 total time elapsed so far: 13.00000 # loops : 180 mean,max change (kT/e) : 1.5021897E-03 2.7271271E-02 energy calculations done at 13.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.14000 DelPhi exited at 11:50:38 13.138u 0.215s 0:13.61 98.0% 0+0k 0+0io 0pf+0w