Wed Dec 28 11:01:54 PST 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 Wed Dec 28 2011 at 11:01:54 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 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: 0.6008337 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): -34.65200 13.12800 ymin,ymax (A): 0.4220001 41.02900 zmin,zma (A): -0.1589999 59.09200 x,y,z range (A): 47.78000 40.60700 59.25100 scale (grids/A): 0.6008337 object centre (A): -10.76200 20.72550 29.46650 number of atom coordinates read : 1946 total number of charged atoms : 1816 net assigned charge : 4.000004 assigned positive charge : 290.5820 centred at (gu) : 89.46371 89.74630 89.05515 assigned negative charge : -286.5823 centred at (gu) : 89.34557 89.92162 89.02834 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 4811 nv = 96 ne = 84 npr = 39703 no. pairs analyzed = 39703 no. exposed pairs = 2451 no. arc points = 17318 no. surface atoms = 838 nbur = 1108 mkacc time = 0.1100000 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 = 1.456000 m= 230 mr = 2632 m= 0 mr = 18 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 2391 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1743 ## 197 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 5830 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2669236E-09 2.0425699E-09 midg,1,midg; midg,igrid,midg 6.9147061E-09 -2.9776350E-09 1,midg,midg; igrid,midg,midg -1.7440006E-09 4.4285740E-09 gauss-seidel spectral radius is 0.9856094 estimated iterations to convergence 68 setup time was (sec) 0.5800000 now iterating at: 11:01:55 rms-change max change #iterations 9.5837981E-02 17.14244 at 10iterations 7.9114661E-03 1.477311 at 20iterations 6.6760019E-04 0.1279068 at 30iterations 5.8220412E-05 1.2420177E-02 at 40iterations 4.9273308E-06 7.5387955E-04 at 50iterations finished qdiffx linear iterations at : 11:01:59 total time elapsed so far: 4.610000 # loops : 50 mean,max change (kT/e) : 4.9273308E-06 7.5387955E-04 energy calculations done at 4.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.800000 DelPhi exited at 11:02:00 4.802u 0.350s 0:05.71 90.1% 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 Wed Dec 28 2011 at 11:02:00 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 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: 1.802501 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): -34.65200 13.12800 ymin,ymax (A): 0.4220001 41.02900 zmin,zma (A): -0.1589999 59.09200 x,y,z range (A): 47.78000 40.60700 59.25100 scale (grids/A): 1.802501 object centre (A): -10.76200 20.72550 29.46650 number of atom coordinates read : 1946 total number of charged atoms : 1816 net assigned charge : 4.000004 assigned positive charge : 290.5820 centred at (gu) : 88.39104 89.23895 87.16541 assigned negative charge : -286.5823 centred at (gu) : 88.03684 89.76501 87.08521 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 52105 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17318 grid for indexing accessible points = 1.400000 m= 18700 mr = 35801 m= 2514 mr = 13975 m= 100 mr = 1480 m= 0 mr = 23 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 22140 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 14197 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) : 0.6008337 object centre at (A) : -10.76200 20.72550 29.46650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6065387E-02 2.2982858E-02 midg,1,midg; midg,igrid,midg 9.1992104E-03 -9.3295733E-03 1,midg,midg; igrid,midg,midg -3.6029404E-03 2.8525323E-03 gauss-seidel spectral radius is 0.9984013 estimated iterations to convergence 198 setup time was (sec) 0.8000000 now iterating at: 11:02:01 rms-change max change #iterations 3.240982 153.3306 at 10iterations 1.423105 56.13641 at 20iterations 0.6246936 24.09639 at 30iterations 0.2752550 10.83919 at 40iterations 0.1207291 4.663443 at 50iterations 5.3105161E-02 1.971773 at 60iterations 2.3252193E-02 0.9205389 at 70iterations 1.0193853E-02 0.3784847 at 80iterations 4.5160325E-03 0.1739311 at 90iterations 1.9886778E-03 7.5378895E-02 at 100iterations 8.7376253E-04 3.2117844E-02 at 110iterations 3.8323915E-04 1.3931274E-02 at 120iterations finished qdiffx linear iterations at : 11:02:11 total time elapsed so far: 11.00000 # loops : 120 mean,max change (kT/e) : 3.8323915E-04 1.3931274E-02 energy calculations done at 11.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.20000 DelPhi exited at 11:02:12 11.201u 0.434s 0:11.97 97.1% 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 Wed Dec 28 2011 at 11:02:12 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.703752 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): -34.65200 13.12800 ymin,ymax (A): 0.4220001 41.02900 zmin,zma (A): -0.1589999 59.09200 x,y,z range (A): 47.78000 40.60700 59.25100 scale (grids/A): 2.703752 object centre (A): -10.76200 20.72550 29.46650 number of atom coordinates read : 1946 total number of charged atoms : 1816 net assigned charge : 4.000004 assigned positive charge : 290.5820 centred at (gu) : 87.58671 88.85849 85.74815 assigned negative charge : -286.5823 centred at (gu) : 87.05522 89.64760 85.62770 start vw surface at 0.1600000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 120613 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17318 grid for indexing accessible points = 1.400000 m= 61089 mr = 86703 m= 21035 mr = 50382 m= 4341 mr = 17163 m= 398 mr = 3154 m= 16 mr = 217 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.260000 number of dielectric boundary points 49873 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 14527 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) : 1.802501 object centre at (A) : -10.76200 20.72550 29.46650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1222155 0.2229567 midg,1,midg; midg,igrid,midg 6.8768792E-02 -0.1315066 1,midg,midg; igrid,midg,midg -7.3102973E-02 3.4997400E-02 gauss-seidel spectral radius is 0.9991738 estimated iterations to convergence 275 setup time was (sec) 1.660000 now iterating at: 11:02:14 rms-change max change #iterations 7.743959 275.2954 at 10iterations 4.347126 132.5212 at 20iterations 2.430468 56.45504 at 30iterations 1.352277 29.33594 at 40iterations 0.7514342 16.54182 at 50iterations 0.4166872 9.361208 at 60iterations 0.2310264 4.940530 at 70iterations 0.1286275 2.665797 at 80iterations 7.1234472E-02 1.557274 at 90iterations 3.9468817E-02 0.9304771 at 100iterations 2.1996403E-02 0.4687500 at 110iterations 1.2191524E-02 0.2678509 at 120iterations 6.7821024E-03 0.1743469 at 130iterations 3.7562093E-03 7.8588486E-02 at 140iterations 2.0898809E-03 4.2392731E-02 at 150iterations 1.1592570E-03 2.6093364E-02 at 160iterations 6.4370013E-04 1.3832092E-02 at 170iterations 3.5716611E-04 7.8485012E-03 at 180iterations finished qdiffx linear iterations at : 11:02:30 total time elapsed so far: 17.80000 # loops : 180 mean,max change (kT/e) : 3.5716611E-04 7.8485012E-03 energy calculations done at 17.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.00000 DelPhi exited at 11:02:32 18.004u 0.475s 0:19.74 93.5% 0+0k 0+0io 0pf+0w