Mon Oct 10 14:04:44 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+sph.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 = amb.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 14:04:44 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4549 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5195185 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): 28.22800 96.75300 ymin,ymax (A): 17.48400 80.75400 zmin,zma (A): 0.9569999 54.90500 x,y,z range (A): 68.52499 63.27000 53.94800 scale (grids/A): 0.5195185 object centre (A): 62.49050 49.11900 27.93100 number of atom coordinates read : 4549 total number of charged atoms : 4388 net assigned charge : 6.000025 assigned positive charge : 690.5654 centred at (gu) : 89.28461 91.34124 89.95486 assigned negative charge : -684.5704 centred at (gu) : 89.19918 91.49680 90.03534 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8030 nv = 96 ne = 84 npr = 87872 no. pairs analyzed = 87872 no. exposed pairs = 6182 no. arc points = 44051 no. surface atoms = 2061 nbur = 2488 mkacc time = 0.2000000 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 = 1.652000 m= 267 mr = 3849 m= 1 mr = 5 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 0.5000000 number of dielectric boundary points 4444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4395 ## 690 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 10754 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2924506E-10 -1.5429981E-10 midg,1,midg; midg,igrid,midg 4.8515691E-10 -6.2505079E-10 1,midg,midg; igrid,midg,midg -2.1210185E-10 3.6700193E-10 gauss-seidel spectral radius is 0.9810482 estimated iterations to convergence 60 setup time was (sec) 0.7400000 now iterating at: 14:04:45 rms-change max change #iterations 7.0652872E-02 15.19984 at 10iterations 4.1929432E-03 0.7620087 at 20iterations 3.7011388E-04 5.4969788E-02 at 30iterations 9.7949785E-05 1.8493652E-02 at 40iterations 3.4500048E-05 6.7811012E-03 at 50iterations finished qdiffx linear iterations at : 14:04:47 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 3.4500048E-05 6.7811012E-03 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 14:04:48 3.622u 0.148s 0:04.09 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 Mon Oct 10 2011 at 14:04:48 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4549 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.558555 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): 28.22800 96.75300 ymin,ymax (A): 17.48400 80.75400 zmin,zma (A): 0.9569999 54.90500 x,y,z range (A): 68.52499 63.27000 53.94800 scale (grids/A): 1.558555 object centre (A): 62.49050 49.11900 27.93100 number of atom coordinates read : 4549 total number of charged atoms : 4388 net assigned charge : 6.000025 assigned positive charge : 690.5654 centred at (gu) : 87.85197 94.02164 89.86264 assigned negative charge : -684.5704 centred at (gu) : 87.59716 94.48991 90.10587 start vw surface at 0.2100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 89787 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44051 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 25864 mr = 59211 m= 2386 mr = 16718 m= 50 mr = 954 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 41204 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 596 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 33103 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) : 0.5195185 object centre at (A) : 62.49050 49.11900 27.93100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0053091E-03 -9.6831964E-03 midg,1,midg; midg,igrid,midg 2.3230344E-02 1.7047849E-02 1,midg,midg; igrid,midg,midg -9.7084057E-04 1.2572419E-02 gauss-seidel spectral radius is 0.9981854 estimated iterations to convergence 186 setup time was (sec) 0.9700000 now iterating at: 14:04:49 rms-change max change #iterations 3.841190 185.5890 at 10iterations 1.588364 56.37169 at 20iterations 0.6607528 23.53761 at 30iterations 0.2748192 8.583573 at 40iterations 0.1146246 3.963814 at 50iterations 4.7641501E-02 1.435593 at 60iterations 1.9907011E-02 0.6125622 at 70iterations 8.2763974E-03 0.2617798 at 80iterations 3.4698686E-03 0.1173325 at 90iterations 1.4629574E-03 5.0214767E-02 at 100iterations 6.2493462E-04 2.3733139E-02 at 110iterations 2.7832316E-04 9.2697144E-03 at 120iterations finished qdiffx linear iterations at : 14:04:56 total time elapsed so far: 8.040000 # loops : 120 mean,max change (kT/e) : 2.7832316E-04 9.2697144E-03 energy calculations done at 8.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.230000 DelPhi exited at 14:04:57 8.234u 0.225s 0:08.84 95.5% 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 14:04:57 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4549 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.337833 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): 28.22800 96.75300 ymin,ymax (A): 17.48400 80.75400 zmin,zma (A): 0.9569999 54.90500 x,y,z range (A): 68.52499 63.27000 53.94800 scale (grids/A): 2.337833 object centre (A): 62.49050 49.11900 27.93100 number of atom coordinates read : 4549 total number of charged atoms : 4388 net assigned charge : 6.000025 assigned positive charge : 690.5654 centred at (gu) : 86.77761 96.03209 89.79380 assigned negative charge : -684.5704 centred at (gu) : 86.39581 96.73486 90.15862 start vw surface at 0.2200000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 208758 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44051 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 92291 mr = 146162 m= 23548 mr = 70415 m= 3191 mr = 16463 m= 198 mr = 1893 m= 2 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.670000 number of dielectric boundary points 92985 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 35011 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) : 1.558555 object centre at (A) : 62.49050 49.11900 27.93100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5582979E-02 -0.1328705 midg,1,midg; midg,igrid,midg 0.3382917 0.4051501 1,midg,midg; igrid,midg,midg 0.1595361 0.2362423 gauss-seidel spectral radius is 0.9991913 estimated iterations to convergence 278 setup time was (sec) 1.990000 now iterating at: 14:04:59 rms-change max change #iterations 10.49013 343.7297 at 10iterations 6.192612 131.6570 at 20iterations 3.589737 77.21671 at 30iterations 2.066800 44.04622 at 40iterations 1.185309 26.32263 at 50iterations 0.6754924 12.76545 at 60iterations 0.3837665 7.546791 at 70iterations 0.2179451 4.180015 at 80iterations 0.1231311 2.372710 at 90iterations 6.9578208E-02 1.459216 at 100iterations 3.9273266E-02 0.7306976 at 110iterations 2.2112017E-02 0.4144211 at 120iterations 1.2464373E-02 0.2391548 at 130iterations 7.0124948E-03 0.1342316 at 140iterations 3.9581084E-03 7.9097748E-02 at 150iterations 2.2363150E-03 4.0699482E-02 at 160iterations 1.2717145E-03 2.5436401E-02 at 170iterations 7.3036196E-04 1.5005112E-02 at 180iterations finished qdiffx linear iterations at : 14:05:10 total time elapsed so far: 12.92000 # loops : 180 mean,max change (kT/e) : 7.3036196E-04 1.5005112E-02 energy calculations done at 12.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.10000 DelPhi exited at 14:05:11 13.104u 0.194s 0:13.82 96.1% 0+0k 0+0io 0pf+0w