Sun Oct 9 12:24:13 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 Sun Oct 9 2011 at 12:24:13 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 = 2420 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: 0.6914098 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): -14.23600 36.91700 ymin,ymax (A): -0.3939999 44.78400 zmin,zma (A): -7.004000 44.48500 x,y,z range (A): 51.15300 45.17800 51.48900 scale (grids/A): 0.6914098 object centre (A): 11.34050 22.19500 18.74050 number of atom coordinates read : 2420 total number of charged atoms : 2278 net assigned charge : 3.500024 assigned positive charge : 370.2410 centred at (gu) : 91.11874 91.42491 90.04405 assigned negative charge : -366.7416 centred at (gu) : 91.32240 91.50195 90.00040 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7739 nv = 96 ne = 84 npr = 48418 no. pairs analyzed = 48418 no. exposed pairs = 3016 no. arc points = 21020 no. surface atoms = 1017 nbur = 1403 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 510 mr = 4320 m= 2 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1 time to turn everything in is 0.3300000 number of dielectric boundary points 3858 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1981 ## 175 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8802 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9739416E-09 3.9394852E-08 midg,1,midg; midg,igrid,midg 3.9470432E-08 -1.3298230E-08 1,midg,midg; igrid,midg,midg 8.1324238E-08 -7.8236702E-08 gauss-seidel spectral radius is 0.9891350 estimated iterations to convergence 78 setup time was (sec) 0.6000000 now iterating at: 12:24:14 rms-change max change #iterations 0.1964684 25.26675 at 10iterations 2.3880189E-02 3.126736 at 20iterations 3.1845691E-03 0.4090996 at 30iterations 6.5064541E-04 9.8007202E-02 at 40iterations 2.0288338E-04 3.2079697E-02 at 50iterations finished qdiffx linear iterations at : 12:24:17 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 2.0288338E-04 3.2079697E-02 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.010000 DelPhi exited at 12:24:18 4.016u 0.257s 0:04.68 91.0% 0+0k 0+0io 4pf+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 Sun Oct 9 2011 at 12:24:18 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 = 2420 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: 2.074229 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): -14.23600 36.91700 ymin,ymax (A): -0.3939999 44.78400 zmin,zma (A): -7.004000 44.48500 x,y,z range (A): 51.15300 45.17800 51.48900 scale (grids/A): 2.074229 object centre (A): 11.34050 22.19500 18.74050 number of atom coordinates read : 2420 total number of charged atoms : 2278 net assigned charge : 3.500024 assigned positive charge : 370.2410 centred at (gu) : 93.35551 94.27419 90.13167 assigned negative charge : -366.7416 centred at (gu) : 93.96696 94.50577 90.00095 start vw surface at 0.1500000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 81974 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21020 grid for indexing accessible points = 1.400000 m= 32655 mr = 56906 m= 6617 mr = 24717 m= 603 mr = 4539 m= 18 mr = 297 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 84 time to turn everything in is 0.7400000 number of dielectric boundary points 35408 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 94 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 18042 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) : 0.6914098 object centre at (A) : 11.34050 22.19500 18.74050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1428691E-02 2.0959057E-02 midg,1,midg; midg,igrid,midg 3.7389349E-02 6.0390960E-03 1,midg,midg; igrid,midg,midg 2.6423702E-02 -5.6204941E-02 gauss-seidel spectral radius is 0.9988229 estimated iterations to convergence 231 setup time was (sec) 1.040000 now iterating at: 12:24:19 rms-change max change #iterations 4.884100 224.0986 at 10iterations 2.407206 83.09666 at 20iterations 1.191297 36.69540 at 30iterations 0.5900702 19.12312 at 40iterations 0.2904412 9.188274 at 50iterations 0.1444933 4.234604 at 60iterations 7.1543798E-02 2.280919 at 70iterations 3.5467912E-02 1.020439 at 80iterations 1.7700527E-02 0.5549812 at 90iterations 8.8865487E-03 0.2612133 at 100iterations 4.4973469E-03 0.1334019 at 110iterations 2.3455627E-03 6.8222046E-02 at 120iterations finished qdiffx linear iterations at : 12:24:28 total time elapsed so far: 9.300000 # loops : 120 mean,max change (kT/e) : 2.3455627E-03 6.8222046E-02 energy calculations done at 9.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.480000 DelPhi exited at 12:24:28 9.482u 0.297s 0:10.34 94.4% 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 Sun Oct 9 2011 at 12:24:28 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 = 2420 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: 3.111344 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): -14.23600 36.91700 ymin,ymax (A): -0.3939999 44.78400 zmin,zma (A): -7.004000 44.48500 x,y,z range (A): 51.15300 45.17800 51.48900 scale (grids/A): 3.111344 object centre (A): 11.34050 22.19500 18.74050 number of atom coordinates read : 2420 total number of charged atoms : 2278 net assigned charge : 3.500024 assigned positive charge : 370.2410 centred at (gu) : 95.03329 96.41116 90.19735 assigned negative charge : -366.7416 centred at (gu) : 95.95031 96.75867 90.00134 start vw surface at 0.1500000 fill in re-entrant regions at 1.040000 boundary points on vw surface= 188934 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21020 grid for indexing accessible points = 1.400000 m= 101132 mr = 137508 m= 42087 mr = 83691 m= 12506 mr = 34685 m= 2645 mr = 9857 m= 223 mr = 1976 m= 2 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 280 time to turn everything in is 2.360000 number of dielectric boundary points 79680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.530000 number of grid points assigned charge 18224 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) : 2.074229 object centre at (A) : 11.34050 22.19500 18.74050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3420390 0.1010749 midg,1,midg; midg,igrid,midg 0.3260977 -7.0944726E-02 1,midg,midg; igrid,midg,midg 0.4502441 -0.5621683 gauss-seidel spectral radius is 0.9992983 estimated iterations to convergence 298 setup time was (sec) 2.700000 now iterating at: 12:24:31 rms-change max change #iterations 10.92816 393.4715 at 10iterations 6.479928 136.0486 at 20iterations 3.815715 71.53051 at 30iterations 2.246042 43.34735 at 40iterations 1.323910 23.13074 at 50iterations 0.7763522 13.02828 at 60iterations 0.4556375 7.862696 at 70iterations 0.2665655 4.551264 at 80iterations 0.1566370 2.601980 at 90iterations 9.1553770E-02 1.516968 at 100iterations 5.3669106E-02 0.9798284 at 110iterations 3.1648502E-02 0.5156174 at 120iterations 1.8734377E-02 0.3782835 at 130iterations 1.1210690E-02 0.1943932 at 140iterations 6.8831402E-03 0.1295776 at 150iterations 4.3887044E-03 8.6154938E-02 at 160iterations 2.9489081E-03 6.2477112E-02 at 170iterations 2.1176226E-03 4.9495697E-02 at 180iterations finished qdiffx linear iterations at : 12:24:46 total time elapsed so far: 16.66000 # loops : 180 mean,max change (kT/e) : 2.1176226E-03 4.9495697E-02 energy calculations done at 16.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.83000 DelPhi exited at 12:24:46 16.836u 0.331s 0:17.91 95.8% 0+0k 0+0io 0pf+0w