Tue Oct 11 07:08:41 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 Tue Oct 11 2011 at 07:08:41 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 = 3808 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5528379 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): -5.761000 54.05100 ymin,ymax (A): -53.03500 -1.840000 zmin,zma (A): -37.38400 27.01100 x,y,z range (A): 59.81200 51.19500 64.39500 scale (grids/A): 0.5528379 object centre (A): 24.14500 -27.43750 -5.186502 number of atom coordinates read : 3808 total number of charged atoms : 3665 net assigned charge : 7.500036 assigned positive charge : 578.1312 centred at (gu) : 90.37779 90.60316 90.54720 assigned negative charge : -570.6336 centred at (gu) : 90.24632 90.60608 90.54284 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 7416 nv = 96 ne = 84 npr = 79561 no. pairs analyzed = 79561 no. exposed pairs = 4310 no. arc points = 30269 no. surface atoms = 1454 nbur = 2354 mkacc time = 0.2200000 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 = 1.568000 m= 288 mr = 4179 m= 1 mr = 16 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 0.4800000 number of dielectric boundary points 3510 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3090 ## 397 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 9747 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.8829085E-10 7.4210632E-10 midg,1,midg; midg,igrid,midg 5.5082278E-10 6.5911709E-10 1,midg,midg; igrid,midg,midg -7.8528828E-10 2.2218878E-09 gauss-seidel spectral radius is 0.9831807 estimated iterations to convergence 63 setup time was (sec) 0.7500000 now iterating at: 07:08:42 rms-change max change #iterations 8.7699361E-02 12.27457 at 10iterations 6.7793163E-03 0.9910126 at 20iterations 8.6682581E-04 0.1531868 at 30iterations 2.2359965E-04 4.1044235E-02 at 40iterations 6.3287429E-05 1.1743546E-02 at 50iterations finished qdiffx linear iterations at : 07:08:46 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 6.3287429E-05 1.1743546E-02 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.250000 DelPhi exited at 07:08:46 4.249u 0.248s 0:05.01 89.4% 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 07:08:46 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 = 3808 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.658514 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): -5.761000 54.05100 ymin,ymax (A): -53.03500 -1.840000 zmin,zma (A): -37.38400 27.01100 x,y,z range (A): 59.81200 51.19500 64.39500 scale (grids/A): 1.658514 object centre (A): 24.14500 -27.43750 -5.186502 number of atom coordinates read : 3808 total number of charged atoms : 3665 net assigned charge : 7.500036 assigned positive charge : 578.1312 centred at (gu) : 91.13172 91.80839 91.64050 assigned negative charge : -570.6336 centred at (gu) : 90.73837 91.81792 91.62807 start vw surface at 0.1900000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 82877 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30269 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 26441 mr = 59033 m= 2576 mr = 18982 m= 62 mr = 1364 m= 0 mr = 4 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 1192 time to turn everything in is 0.7300000 number of dielectric boundary points 32573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 349 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 28095 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) : 0.5528379 object centre at (A) : 24.14500 -27.43750 -5.186502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4221951E-02 5.4692868E-02 midg,1,midg; midg,igrid,midg -8.7870713E-03 -5.8929403E-03 1,midg,midg; igrid,midg,midg -1.6187960E-02 1.8129064E-02 gauss-seidel spectral radius is 0.9983202 estimated iterations to convergence 194 setup time was (sec) 1.030000 now iterating at: 07:08:48 rms-change max change #iterations 3.926022 183.1729 at 10iterations 1.697179 51.41684 at 20iterations 0.7341241 23.69145 at 30iterations 0.3169494 12.54776 at 40iterations 0.1372102 4.152390 at 50iterations 5.9366122E-02 1.938994 at 60iterations 2.5695866E-02 0.7817316 at 70iterations 1.1097557E-02 0.3618126 at 80iterations 4.8393891E-03 0.1593037 at 90iterations 2.1280677E-03 7.2269440E-02 at 100iterations 9.5486670E-04 3.2260895E-02 at 110iterations 4.3927808E-04 1.7387390E-02 at 120iterations finished qdiffx linear iterations at : 07:08:56 total time elapsed so far: 9.430000 # loops : 120 mean,max change (kT/e) : 4.3927808E-04 1.7387390E-02 energy calculations done at 9.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.600000 DelPhi exited at 07:08:57 9.606u 0.298s 0:10.17 97.2% 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 Tue Oct 11 2011 at 07:08:57 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 = 3808 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.487771 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): -5.761000 54.05100 ymin,ymax (A): -53.03500 -1.840000 zmin,zma (A): -37.38400 27.01100 x,y,z range (A): 59.81200 51.19500 64.39500 scale (grids/A): 2.487771 object centre (A): 24.14500 -27.43750 -5.186502 number of atom coordinates read : 3808 total number of charged atoms : 3665 net assigned charge : 7.500036 assigned positive charge : 578.1312 centred at (gu) : 91.69718 92.71214 92.46040 assigned negative charge : -570.6336 centred at (gu) : 91.10760 92.72683 92.44196 start vw surface at 0.2000000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 192705 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30269 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 91961 mr = 143695 m= 26356 mr = 74872 m= 4019 mr = 20430 m= 249 mr = 2751 m= 4 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 3788 time to turn everything in is 1.790000 number of dielectric boundary points 73449 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.950000 number of grid points assigned charge 29300 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) : 1.658514 object centre at (A) : 24.14500 -27.43750 -5.186502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3714550 1.364038 midg,1,midg; midg,igrid,midg -0.1436082 -0.1134677 1,midg,midg; igrid,midg,midg -0.2551394 0.2759755 gauss-seidel spectral radius is 0.9991937 estimated iterations to convergence 278 setup time was (sec) 2.120000 now iterating at: 07:08:59 rms-change max change #iterations 9.963657 268.2068 at 10iterations 5.653445 156.5315 at 20iterations 3.200777 66.62581 at 30iterations 1.812312 36.29412 at 40iterations 1.022293 20.50773 at 50iterations 0.5752453 11.58991 at 60iterations 0.3236541 6.023834 at 70iterations 0.1818744 3.198872 at 80iterations 0.1021290 1.906064 at 90iterations 5.7281148E-02 1.035034 at 100iterations 3.2171529E-02 0.5881157 at 110iterations 1.8065190E-02 0.3308887 at 120iterations 1.0145754E-02 0.2050457 at 130iterations 5.6902291E-03 0.1027393 at 140iterations 3.2063928E-03 6.7756653E-02 at 150iterations 1.8033872E-03 3.3737183E-02 at 160iterations 1.0168996E-03 1.8595695E-02 at 170iterations 5.7887245E-04 1.0097504E-02 at 180iterations finished qdiffx linear iterations at : 07:09:13 total time elapsed so far: 15.95000 # loops : 180 mean,max change (kT/e) : 5.7887245E-04 1.0097504E-02 energy calculations done at 15.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.13000 DelPhi exited at 07:09:14 16.128u 0.317s 0:16.98 96.7% 0+0k 0+0io 0pf+0w