Sun Oct 9 07:31:19 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 Sun Oct 9 2011 at 07:31:19 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2513 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5757630 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): -4.485000 50.22000 ymin,ymax (A): 6.518000 57.21400 zmin,zma (A): 53.24000 115.0710 x,y,z range (A): 54.70500 50.69600 61.83100 scale (grids/A): 0.5757630 object centre (A): 22.86750 31.86600 84.15550 number of atom coordinates read : 2513 total number of charged atoms : 2368 net assigned charge : -11.49998 assigned positive charge : 376.2619 centred at (gu) : 89.94685 90.35828 87.92490 assigned negative charge : -387.7623 centred at (gu) : 89.83389 90.70811 87.71406 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5451 nv = 96 ne = 84 npr = 50303 no. pairs analyzed = 50303 no. exposed pairs = 3464 no. arc points = 24699 no. surface atoms = 1173 nbur = 1340 mkacc time = 0.1100000 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= 230 mr = 2577 m= 0 mr = 13 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2566 ## 301 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7009 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.2137444E-09 8.0808482E-10 midg,1,midg; midg,igrid,midg 3.2263558E-09 -8.7940935E-09 1,midg,midg; igrid,midg,midg -3.9782675E-09 -1.8648404E-10 gauss-seidel spectral radius is 0.9844010 estimated iterations to convergence 66 setup time was (sec) 0.5300000 now iterating at: 07:31:19 rms-change max change #iterations 8.4975131E-02 15.31362 at 10iterations 6.3667661E-03 1.193212 at 20iterations 4.7818210E-04 8.9066744E-02 at 30iterations 3.7132806E-05 6.6986084E-03 at 40iterations 2.9373516E-06 4.5585632E-04 at 50iterations finished qdiffx linear iterations at : 07:31:22 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 2.9373516E-06 4.5585632E-04 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 07:31:23 3.394u 0.204s 0:03.85 93.2% 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 Sun Oct 9 2011 at 07:31:23 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2513 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.727289 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): -4.485000 50.22000 ymin,ymax (A): 6.518000 57.21400 zmin,zma (A): 53.24000 115.0710 x,y,z range (A): 54.70500 50.69600 61.83100 scale (grids/A): 1.727289 object centre (A): 22.86750 31.86600 84.15550 number of atom coordinates read : 2513 total number of charged atoms : 2368 net assigned charge : -11.49998 assigned positive charge : 376.2619 centred at (gu) : 89.83981 91.07443 83.77411 assigned negative charge : -387.7623 centred at (gu) : 89.50127 92.12401 83.14172 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 58800 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24699 grid for indexing accessible points = 1.400000 m= 18593 mr = 37112 m= 2090 mr = 12654 m= 39 mr = 1103 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 417 time to turn everything in is 0.4500000 number of dielectric boundary points 28651 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 222 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 18325 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) : 0.5757630 object centre at (A) : 22.86750 31.86600 84.15550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0299322E-02 1.0763420E-02 midg,1,midg; midg,igrid,midg 6.6173926E-04 -3.6255568E-02 1,midg,midg; igrid,midg,midg -2.5863901E-02 -1.6402662E-02 gauss-seidel spectral radius is 0.9983324 estimated iterations to convergence 194 setup time was (sec) 0.7500000 now iterating at: 07:31:24 rms-change max change #iterations 3.428655 198.9945 at 10iterations 1.472939 56.72823 at 20iterations 0.6356695 26.43016 at 30iterations 0.2745709 10.36201 at 40iterations 0.1183799 4.310501 at 50iterations 5.0929837E-02 1.907139 at 60iterations 2.1983901E-02 0.8122292 at 70iterations 9.5181679E-03 0.3522797 at 80iterations 4.1058888E-03 0.1454773 at 90iterations 1.7795732E-03 6.3658714E-02 at 100iterations 7.6660857E-04 2.8533936E-02 at 110iterations 3.3060962E-04 1.1879921E-02 at 120iterations finished qdiffx linear iterations at : 07:31:30 total time elapsed so far: 7.440000 # loops : 120 mean,max change (kT/e) : 3.3060962E-04 1.1879921E-02 energy calculations done at 7.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 07:31:31 7.630u 0.216s 0:08.13 96.4% 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 07:31:31 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2513 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.590934 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): -4.485000 50.22000 ymin,ymax (A): 6.518000 57.21400 zmin,zma (A): 53.24000 115.0710 x,y,z range (A): 54.70500 50.69600 61.83100 scale (grids/A): 2.590934 object centre (A): 22.86750 31.86600 84.15550 number of atom coordinates read : 2513 total number of charged atoms : 2368 net assigned charge : -11.49998 assigned positive charge : 376.2619 centred at (gu) : 89.75980 91.61151 80.66105 assigned negative charge : -387.7623 centred at (gu) : 89.25193 93.18594 79.71257 start vw surface at 0.1500000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 136038 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24699 grid for indexing accessible points = 1.400000 m= 62518 mr = 91003 m= 19401 mr = 48628 m= 3310 mr = 14822 m= 193 mr = 2185 m= 3 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.5699999 no. cavity mid-points inaccessible to solvent = 1381 time to turn everything in is 1.060000 number of dielectric boundary points 64722 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 18933 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) : 1.727289 object centre at (A) : 22.86750 31.86600 84.15550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4692291 -5.1954471E-02 midg,1,midg; midg,igrid,midg 3.2997753E-02 -0.4253757 1,midg,midg; igrid,midg,midg -0.1928278 -0.2538697 gauss-seidel spectral radius is 0.9991811 estimated iterations to convergence 276 setup time was (sec) 1.380000 now iterating at: 07:31:32 rms-change max change #iterations 8.739412 340.2617 at 10iterations 5.003098 121.1255 at 20iterations 2.843333 76.07948 at 30iterations 1.604669 38.92519 at 40iterations 0.9061000 24.42093 at 50iterations 0.5090921 11.33097 at 60iterations 0.2856812 6.950466 at 70iterations 0.1603417 3.453667 at 80iterations 8.9892194E-02 1.998757 at 90iterations 5.0216533E-02 1.061672 at 100iterations 2.8079690E-02 0.5784569 at 110iterations 1.5712719E-02 0.3529835 at 120iterations 8.7540243E-03 0.1793444 at 130iterations 4.8887031E-03 0.1025435 at 140iterations 2.7285789E-03 5.6396961E-02 at 150iterations 1.5212225E-03 3.3224106E-02 at 160iterations 8.4941043E-04 2.1890640E-02 at 170iterations 4.7360425E-04 1.0330200E-02 at 180iterations finished qdiffx linear iterations at : 07:31:43 total time elapsed so far: 12.12000 # loops : 180 mean,max change (kT/e) : 4.7360425E-04 1.0330200E-02 energy calculations done at 12.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.31000 DelPhi exited at 07:31:44 12.309u 0.261s 0:12.84 97.8% 0+0k 0+0io 0pf+0w