Sat Oct 15 10:21:57 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+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 15 2011 at 10:21:57 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 = 2720 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: 0.5663559 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): -21.87700 33.04400 ymin,ymax (A): -21.38000 26.25200 zmin,zma (A): 2.428000 65.28600 x,y,z range (A): 54.92100 47.63200 62.85800 scale (grids/A): 0.5663559 object centre (A): 5.583499 2.436001 33.85700 number of atom coordinates read : 2720 total number of charged atoms : 2569 net assigned charge : 6.7800283E-06 assigned positive charge : 398.3474 centred at (gu) : 89.72076 90.78094 92.67474 assigned negative charge : -398.3483 centred at (gu) : 89.63084 90.78103 92.60815 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5661 nv = 96 ne = 84 npr = 54607 no. pairs analyzed = 54607 no. exposed pairs = 3627 no. arc points = 25622 no. surface atoms = 1230 nbur = 1490 mkacc time = 0.1800000 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 = 1.512000 m= 218 mr = 2733 m= 0 mr = 5 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3141 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2641 ## 326 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 7385 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.4550952E-10 1.5356310E-09 midg,1,midg; midg,igrid,midg -1.6009269E-11 -2.5908643E-11 1,midg,midg; igrid,midg,midg -1.2188690E-09 1.0031567E-09 gauss-seidel spectral radius is 0.9838999 estimated iterations to convergence 65 setup time was (sec) 0.6800000 now iterating at: 10:21:58 rms-change max change #iterations 8.0736138E-02 14.77240 at 10iterations 5.9570037E-03 1.034817 at 20iterations 4.3807493E-04 7.3582649E-02 at 30iterations 3.2968404E-05 5.8794022E-03 at 40iterations 2.6881862E-06 4.5585632E-04 at 50iterations finished qdiffx linear iterations at : 10:22:02 total time elapsed so far: 4.680000 # loops : 50 mean,max change (kT/e) : 2.6881862E-06 4.5585632E-04 energy calculations done at 4.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.900000 DelPhi exited at 10:22:03 4.900u 0.462s 0:06.54 81.9% 0+0k 0+0io 3pf+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 15 2011 at 10:22:04 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 = 2720 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: 1.699068 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): -21.87700 33.04400 ymin,ymax (A): -21.38000 26.25200 zmin,zma (A): 2.428000 65.28600 x,y,z range (A): 54.92100 47.63200 62.85800 scale (grids/A): 1.699068 object centre (A): 5.583499 2.436001 33.85700 number of atom coordinates read : 2720 total number of charged atoms : 2569 net assigned charge : 6.7800283E-06 assigned positive charge : 398.3474 centred at (gu) : 89.16158 92.34203 98.02348 assigned negative charge : -398.3483 centred at (gu) : 88.89221 92.34293 97.82420 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 62177 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25622 grid for indexing accessible points = 1.400000 m= 18282 mr = 40348 m= 1947 mr = 12100 m= 43 mr = 901 m= 0 mr = 4 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 29096 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 253 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 19844 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) : 0.5663559 object centre at (A) : 5.583499 2.436001 33.85700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9674131E-02 3.2891009E-02 midg,1,midg; midg,igrid,midg -7.8001356E-04 -4.4641076E-03 1,midg,midg; igrid,midg,midg -2.6453028E-03 8.7596243E-03 gauss-seidel spectral radius is 0.9983018 estimated iterations to convergence 193 setup time was (sec) 1.010000 now iterating at: 10:22:05 rms-change max change #iterations 3.377646 153.2274 at 10iterations 1.434561 58.17999 at 20iterations 0.6134318 25.40392 at 30iterations 0.2631652 10.50801 at 40iterations 0.1123772 4.241875 at 50iterations 4.8148710E-02 1.770106 at 60iterations 2.0644905E-02 0.8507285 at 70iterations 8.8301282E-03 0.3038259 at 80iterations 3.8089366E-03 0.1361592 at 90iterations 1.6227979E-03 6.9515228E-02 at 100iterations 6.9800398E-04 2.6842117E-02 at 110iterations 2.9883618E-04 1.1226654E-02 at 120iterations finished qdiffx linear iterations at : 10:22:16 total time elapsed so far: 11.72000 # loops : 120 mean,max change (kT/e) : 2.9883618E-04 1.1226654E-02 energy calculations done at 11.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.93000 DelPhi exited at 10:22:17 11.936u 0.493s 0:12.74 97.4% 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 Sat Oct 15 2011 at 10:22:17 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 = 2720 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: 2.548602 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): -21.87700 33.04400 ymin,ymax (A): -21.38000 26.25200 zmin,zma (A): 2.428000 65.28600 x,y,z range (A): 54.92100 47.63200 62.85800 scale (grids/A): 2.548602 object centre (A): 5.583499 2.436001 33.85700 number of atom coordinates read : 2720 total number of charged atoms : 2569 net assigned charge : 6.7800283E-06 assigned positive charge : 398.3474 centred at (gu) : 88.74210 93.51292 102.0351 assigned negative charge : -398.3483 centred at (gu) : 88.33820 93.51440 101.7361 start vw surface at 0.1700000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 144546 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25622 grid for indexing accessible points = 1.400000 m= 62857 mr = 99386 m= 18066 mr = 48569 m= 3038 mr = 13051 m= 217 mr = 1974 m= 6 mr = 92 m= 0 mr = 2 time to grow re-entrant surface = 0.9300001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.610000 number of dielectric boundary points 65656 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 20527 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) : 1.699068 object centre at (A) : 5.583499 2.436001 33.85700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5202441 0.5183520 midg,1,midg; midg,igrid,midg 4.9247597E-03 -8.4763907E-02 1,midg,midg; igrid,midg,midg -6.5984927E-02 9.9653527E-02 gauss-seidel spectral radius is 0.9991692 estimated iterations to convergence 274 setup time was (sec) 2.000000 now iterating at: 10:22:19 rms-change max change #iterations 8.553381 307.8578 at 10iterations 4.836509 121.0268 at 20iterations 2.717355 59.44553 at 30iterations 1.523860 34.05957 at 40iterations 0.8523185 19.38844 at 50iterations 0.4752446 10.07264 at 60iterations 0.2649354 5.735064 at 70iterations 0.1474820 3.316055 at 80iterations 8.2070895E-02 1.786463 at 90iterations 4.5573130E-02 0.9515381 at 100iterations 2.5321133E-02 0.5321484 at 110iterations 1.4044236E-02 0.3171768 at 120iterations 7.8087468E-03 0.2073669 at 130iterations 4.3309322E-03 8.8006973E-02 at 140iterations 2.4106628E-03 5.1054001E-02 at 150iterations 1.3351773E-03 2.9104233E-02 at 160iterations 7.4320531E-04 1.4993668E-02 at 170iterations 4.1309564E-04 8.3198547E-03 at 180iterations finished qdiffx linear iterations at : 10:22:36 total time elapsed so far: 19.12000 # loops : 180 mean,max change (kT/e) : 4.1309564E-04 8.3198547E-03 energy calculations done at 19.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.33000 DelPhi exited at 10:22:37 19.334u 0.495s 0:20.13 98.4% 0+0k 0+0io 0pf+0w