Sat Oct 8 21:42:08 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 Sat Oct 8 2011 at 21:42:08 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 = 2028 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6652340 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): 5.639000 59.15400 ymin,ymax (A): 2.665000 49.63000 zmin,zma (A): 14.72500 55.69500 x,y,z range (A): 53.51500 46.96500 40.97000 scale (grids/A): 0.6652340 object centre (A): 32.39650 26.14750 35.21000 number of atom coordinates read : 2028 total number of charged atoms : 1906 net assigned charge : 1.000005 assigned positive charge : 304.3427 centred at (gu) : 87.70179 89.54129 89.18201 assigned negative charge : -303.3429 centred at (gu) : 87.84846 89.56452 89.18043 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6189 nv = 96 ne = 84 npr = 39882 no. pairs analyzed = 39882 no. exposed pairs = 2690 no. arc points = 18824 no. surface atoms = 907 nbur = 1121 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 385 mr = 3340 m= 1 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3188 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1720 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7032 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3041344E-09 2.1492594E-09 midg,1,midg; midg,igrid,midg 6.9406410E-09 -1.6615107E-09 1,midg,midg; igrid,midg,midg 4.5002064E-08 -1.4776193E-08 gauss-seidel spectral radius is 0.9882377 estimated iterations to convergence 75 setup time was (sec) 0.5500000 now iterating at: 21:42:09 rms-change max change #iterations 0.1467496 25.63192 at 10iterations 1.6974736E-02 2.777084 at 20iterations 2.8968381E-03 0.5208511 at 30iterations 9.0229488E-04 0.1887360 at 40iterations 3.3492656E-04 6.9953918E-02 at 50iterations finished qdiffx linear iterations at : 21:42:13 total time elapsed so far: 4.240000 # loops : 50 mean,max change (kT/e) : 3.3492656E-04 6.9953918E-02 energy calculations done at 4.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.420000 DelPhi exited at 21:42:13 4.422u 0.401s 0:05.10 94.5% 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 Sat Oct 8 2011 at 21:42:13 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 = 2028 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.995702 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): 5.639000 59.15400 ymin,ymax (A): 2.665000 49.63000 zmin,zma (A): 14.72500 55.69500 x,y,z range (A): 53.51500 46.96500 40.97000 scale (grids/A): 1.995702 object centre (A): 32.39650 26.14750 35.21000 number of atom coordinates read : 2028 total number of charged atoms : 1906 net assigned charge : 1.000005 assigned positive charge : 304.3427 centred at (gu) : 83.10524 88.62371 87.54588 assigned negative charge : -303.3429 centred at (gu) : 83.54536 88.69347 87.54119 start vw surface at 0.1000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 65713 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18824 grid for indexing accessible points = 1.400000 m= 24374 mr = 44809 m= 4151 mr = 17644 m= 276 mr = 2486 m= 2 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 29513 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 74 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 15051 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) : 0.6652340 object centre at (A) : 32.39650 26.14750 35.21000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7962149E-03 2.2127631E-03 midg,1,midg; midg,igrid,midg 2.0857928E-02 1.1079940E-03 1,midg,midg; igrid,midg,midg -3.1027839E-02 -4.0756620E-02 gauss-seidel spectral radius is 0.9986981 estimated iterations to convergence 220 setup time was (sec) 0.9000000 now iterating at: 21:42:15 rms-change max change #iterations 4.048960 284.5071 at 10iterations 1.930272 76.56752 at 20iterations 0.9159663 38.01087 at 30iterations 0.4367692 15.49060 at 40iterations 0.2092017 7.162562 at 50iterations 0.1002309 3.679382 at 60iterations 4.8263550E-02 1.567276 at 70iterations 2.3311697E-02 0.8336773 at 80iterations 1.1540701E-02 0.3715439 at 90iterations 5.9706089E-03 0.2179337 at 100iterations 3.3019688E-03 0.1383896 at 110iterations 1.9839951E-03 7.9475403E-02 at 120iterations finished qdiffx linear iterations at : 21:42:24 total time elapsed so far: 10.23000 # loops : 120 mean,max change (kT/e) : 1.9839951E-03 7.9475403E-02 energy calculations done at 10.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.41000 DelPhi exited at 21:42:24 10.410u 0.437s 0:11.14 97.3% 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 Sat Oct 8 2011 at 21:42:24 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2028 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: 2.993553 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): 5.639000 59.15400 ymin,ymax (A): 2.665000 49.63000 zmin,zma (A): 14.72500 55.69500 x,y,z range (A): 53.51500 46.96500 40.97000 scale (grids/A): 2.993553 object centre (A): 32.39650 26.14750 35.21000 number of atom coordinates read : 2028 total number of charged atoms : 1906 net assigned charge : 1.000005 assigned positive charge : 304.3427 centred at (gu) : 79.65798 87.93556 86.31877 assigned negative charge : -303.3429 centred at (gu) : 80.31806 88.04019 86.31165 start vw surface at 0.1100000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 151340 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18824 grid for indexing accessible points = 1.400000 m= 77313 mr = 108187 m= 29523 mr = 62606 m= 7567 mr = 23353 m= 1079 mr = 5441 m= 53 mr = 610 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.450000 number of dielectric boundary points 66660 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 15248 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) : 1.995702 object centre at (A) : 32.39650 26.14750 35.21000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9359496E-02 4.6657557E-03 midg,1,midg; midg,igrid,midg 0.2060499 -7.4769981E-02 1,midg,midg; igrid,midg,midg -0.5886932 -0.5427624 gauss-seidel spectral radius is 0.9992695 estimated iterations to convergence 292 setup time was (sec) 1.770000 now iterating at: 21:42:27 rms-change max change #iterations 9.481976 356.6866 at 10iterations 5.623526 129.2789 at 20iterations 3.301900 73.89530 at 30iterations 1.937260 42.61314 at 40iterations 1.131137 23.98050 at 50iterations 0.6601592 12.74475 at 60iterations 0.3843168 7.996516 at 70iterations 0.2230743 4.460118 at 80iterations 0.1293766 2.421994 at 90iterations 7.5109765E-02 1.500072 at 100iterations 4.3441266E-02 0.8143945 at 110iterations 2.5196873E-02 0.4525719 at 120iterations 1.4655856E-02 0.2908974 at 130iterations 8.5579837E-03 0.1639872 at 140iterations 5.0295861E-03 0.1084585 at 150iterations 3.0199306E-03 6.6009521E-02 at 160iterations 1.8779327E-03 4.3060303E-02 at 170iterations 1.2274687E-03 2.9090881E-02 at 180iterations finished qdiffx linear iterations at : 21:42:42 total time elapsed so far: 17.45000 # loops : 180 mean,max change (kT/e) : 1.2274687E-03 2.9090881E-02 energy calculations done at 17.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.62000 DelPhi exited at 21:42:43 17.626u 0.491s 0:18.39 98.4% 0+0k 0+0io 0pf+0w