Tue Oct 11 08:33:57 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 Tue Oct 11 2011 at 08:33:58 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2644 !!! WARNING: HIR 57 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: 0.6403108 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): -65.72200 -14.52900 ymin,ymax (A): -46.43200 0.6339999 zmin,zma (A): 4.571000 60.16900 x,y,z range (A): 51.19300 47.06600 55.59800 scale (grids/A): 0.6403108 object centre (A): -40.12550 -22.89900 32.37000 number of atom coordinates read : 2644 total number of charged atoms : 2501 net assigned charge : 11.01403 assigned positive charge : 404.2169 centred at (gu) : 89.34502 89.55584 91.44175 assigned negative charge : -393.2035 centred at (gu) : 89.34371 89.28213 91.39630 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7145 nv = 96 ne = 84 npr = 53465 no. pairs analyzed = 53465 no. exposed pairs = 3170 no. arc points = 21972 no. surface atoms = 1072 nbur = 1572 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 340 mr = 3961 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3481 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2266 ## 224 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8680 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.1319049E-09 2.9340544E-08 midg,1,midg; midg,igrid,midg -1.9123682E-08 4.3516621E-08 1,midg,midg; igrid,midg,midg 1.8448112E-08 1.4347320E-08 gauss-seidel spectral radius is 0.9873629 estimated iterations to convergence 73 setup time was (sec) 0.5300000 now iterating at: 08:33:58 rms-change max change #iterations 0.1498928 21.75831 at 10iterations 1.4793081E-02 2.235266 at 20iterations 1.4746153E-03 0.1997681 at 30iterations 1.5022849E-04 1.9714355E-02 at 40iterations 1.8444380E-05 2.5024414E-03 at 50iterations finished qdiffx linear iterations at : 08:34:01 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 1.8444380E-05 2.5024414E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 08:34:01 3.140u 0.131s 0:03.60 90.8% 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 Tue Oct 11 2011 at 08:34:01 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2644 !!! WARNING: HIR 57 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: 1.920932 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): -65.72200 -14.52900 ymin,ymax (A): -46.43200 0.6339999 zmin,zma (A): 4.571000 60.16900 x,y,z range (A): 51.19300 47.06600 55.59800 scale (grids/A): 1.920932 object centre (A): -40.12550 -22.89900 32.37000 number of atom coordinates read : 2644 total number of charged atoms : 2501 net assigned charge : 11.01403 assigned positive charge : 404.2169 centred at (gu) : 88.03467 88.66685 94.32490 assigned negative charge : -393.2035 centred at (gu) : 88.03093 87.84612 94.18869 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 76400 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21972 grid for indexing accessible points = 1.400000 m= 28639 mr = 53487 m= 4596 mr = 21468 m= 237 mr = 2921 m= 2 mr = 66 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 0.5300000 number of dielectric boundary points 31932 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 19670 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) : 0.6403108 object centre at (A) : -40.12550 -22.89900 32.37000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2557156E-02 5.0907280E-02 midg,1,midg; midg,igrid,midg -1.4654071E-02 5.9206020E-02 1,midg,midg; igrid,midg,midg 2.0961661E-02 -5.7659224E-03 gauss-seidel spectral radius is 0.9986598 estimated iterations to convergence 216 setup time was (sec) 0.7900000 now iterating at: 08:34:02 rms-change max change #iterations 4.384311 203.7346 at 10iterations 2.069183 71.87370 at 20iterations 0.9799516 32.64219 at 30iterations 0.4615576 16.76670 at 40iterations 0.2184342 7.580359 at 50iterations 0.1031319 3.259470 at 60iterations 4.8809852E-02 1.640358 at 70iterations 2.3098944E-02 0.7421465 at 80iterations 1.0901240E-02 0.3347187 at 90iterations 5.1620617E-03 0.1580315 at 100iterations 2.4424696E-03 8.3297729E-02 at 110iterations 1.1551840E-03 3.5331726E-02 at 120iterations finished qdiffx linear iterations at : 08:34:08 total time elapsed so far: 6.900000 # loops : 120 mean,max change (kT/e) : 1.1551840E-03 3.5331726E-02 energy calculations done at 6.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.070000 DelPhi exited at 08:34:09 7.074u 0.173s 0:07.62 95.0% 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 Tue Oct 11 2011 at 08:34:09 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2644 !!! WARNING: HIR 57 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: 2.881398 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): -65.72200 -14.52900 ymin,ymax (A): -46.43200 0.6339999 zmin,zma (A): 4.571000 60.16900 x,y,z range (A): 51.19300 47.06600 55.59800 scale (grids/A): 2.881398 object centre (A): -40.12550 -22.89900 32.37000 number of atom coordinates read : 2644 total number of charged atoms : 2501 net assigned charge : 11.01403 assigned positive charge : 404.2169 centred at (gu) : 87.05186 87.99998 96.48715 assigned negative charge : -393.2035 centred at (gu) : 87.04638 86.76913 96.28297 start vw surface at 0.1700000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 176501 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21972 grid for indexing accessible points = 1.400000 m= 91439 mr = 129258 m= 34485 mr = 75427 m= 8092 mr = 28102 m= 1022 mr = 6083 m= 48 mr = 643 m= 0 mr = 16 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.370000 number of dielectric boundary points 72058 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 20008 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) : 1.920932 object centre at (A) : -40.12550 -22.89900 32.37000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2921828 0.1750095 midg,1,midg; midg,igrid,midg -0.1415699 0.5364695 1,midg,midg; igrid,midg,midg 0.1023493 -3.5065044E-02 gauss-seidel spectral radius is 0.9992626 estimated iterations to convergence 291 setup time was (sec) 1.640000 now iterating at: 08:34:11 rms-change max change #iterations 10.23344 412.9615 at 10iterations 6.012421 144.7181 at 20iterations 3.510244 82.04207 at 30iterations 2.038460 42.36089 at 40iterations 1.187749 25.54768 at 50iterations 0.6892940 15.25336 at 60iterations 0.3982383 7.485594 at 70iterations 0.2307556 4.496769 at 80iterations 0.1332492 2.483480 at 90iterations 7.6794066E-02 1.441437 at 100iterations 4.4392128E-02 0.8277345 at 110iterations 2.5602780E-02 0.4837160 at 120iterations 1.4776533E-02 0.2557030 at 130iterations 8.5410308E-03 0.1571698 at 140iterations 4.9146670E-03 8.7074280E-02 at 150iterations 2.8314940E-03 5.0057411E-02 at 160iterations 1.6376956E-03 3.0927658E-02 at 170iterations 9.4431452E-04 1.6914368E-02 at 180iterations finished qdiffx linear iterations at : 08:34:20 total time elapsed so far: 11.09000 # loops : 180 mean,max change (kT/e) : 9.4431452E-04 1.6914368E-02 energy calculations done at 11.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.26000 DelPhi exited at 08:34:21 11.261u 0.176s 0:11.94 95.7% 0+0k 0+0io 0pf+0w