Sun Oct 9 16:15:41 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+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 16:15:41 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3070 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: 0.6209230 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): -21.09900 35.18600 ymin,ymax (A): 54.63300 106.7150 zmin,zma (A): -1.541000 55.79300 x,y,z range (A): 56.28500 52.08200 57.33400 scale (grids/A): 0.6209230 object centre (A): 7.043499 80.67400 27.12600 number of atom coordinates read : 3070 total number of charged atoms : 2928 net assigned charge : -3.499987 assigned positive charge : 457.8630 centred at (gu) : 90.88604 90.31262 89.95644 assigned negative charge : -461.3643 centred at (gu) : 90.90574 90.18385 90.05590 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7788 nv = 96 ne = 84 npr = 63028 no. pairs analyzed = 63028 no. exposed pairs = 3994 no. arc points = 28209 no. surface atoms = 1344 nbur = 1726 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 413 mr = 4022 m= 5 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 38 time to turn everything in is 0.2300000 number of dielectric boundary points 4137 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2765 ## 265 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9666 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1217608E-09 -1.0965039E-08 midg,1,midg; midg,igrid,midg -1.2608096E-08 7.9380689E-09 1,midg,midg; igrid,midg,midg -1.1041662E-09 -5.4733356E-09 gauss-seidel spectral radius is 0.9866120 estimated iterations to convergence 71 setup time was (sec) 0.4300000 now iterating at: 16:15:42 rms-change max change #iterations 0.1385825 21.64352 at 10iterations 1.2936739E-02 1.836490 at 20iterations 1.2553306E-03 0.1566725 at 30iterations 1.5739682E-04 1.9549370E-02 at 40iterations 3.8630766E-05 5.2605867E-03 at 50iterations finished qdiffx linear iterations at : 16:15:45 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 3.8630766E-05 5.2605867E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 16:15:45 3.403u 0.173s 0:03.84 92.9% 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 16:15:45 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3070 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: 1.862769 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): -21.09900 35.18600 ymin,ymax (A): 54.63300 106.7150 zmin,zma (A): -1.541000 55.79300 x,y,z range (A): 56.28500 52.08200 57.33400 scale (grids/A): 1.862769 object centre (A): 7.043499 80.67400 27.12600 number of atom coordinates read : 3070 total number of charged atoms : 2928 net assigned charge : -3.499987 assigned positive charge : 457.8630 centred at (gu) : 92.65749 90.93706 89.86859 assigned negative charge : -461.3643 centred at (gu) : 92.71684 90.55122 90.16727 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 83940 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28209 grid for indexing accessible points = 1.400000 m= 28699 mr = 56461 m= 4575 mr = 20188 m= 245 mr = 2769 m= 2 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 861 time to turn everything in is 0.4200000 number of dielectric boundary points 37965 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 194 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 22947 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) : 0.6209230 object centre at (A) : 7.043499 80.67400 27.12600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2013660E-02 -2.1045098E-02 midg,1,midg; midg,igrid,midg -1.9116709E-02 -1.1766576E-02 1,midg,midg; igrid,midg,midg -1.3712358E-02 -4.1180044E-02 gauss-seidel spectral radius is 0.9986280 estimated iterations to convergence 214 setup time was (sec) 0.6400000 now iterating at: 16:15:46 rms-change max change #iterations 4.443842 158.5635 at 10iterations 2.069268 63.32959 at 20iterations 0.9650187 33.00787 at 30iterations 0.4497101 13.01746 at 40iterations 0.2099371 6.581336 at 50iterations 9.7792685E-02 3.323072 at 60iterations 4.5726392E-02 1.328529 at 70iterations 2.1405855E-02 0.6401482 at 80iterations 9.9939685E-03 0.3171487 at 90iterations 4.6772473E-03 0.1491623 at 100iterations 2.1825279E-03 6.5834045E-02 at 110iterations 1.0255950E-03 2.8419495E-02 at 120iterations finished qdiffx linear iterations at : 16:15:53 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 1.0255950E-03 2.8419495E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 16:15:53 7.856u 0.197s 0:08.33 96.5% 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 Sun Oct 9 2011 at 16:15:53 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3070 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: 2.794154 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): -21.09900 35.18600 ymin,ymax (A): 54.63300 106.7150 zmin,zma (A): -1.541000 55.79300 x,y,z range (A): 56.28500 52.08200 57.33400 scale (grids/A): 2.794154 object centre (A): 7.043499 80.67400 27.12600 number of atom coordinates read : 3070 total number of charged atoms : 2928 net assigned charge : -3.499987 assigned positive charge : 457.8630 centred at (gu) : 93.98605 91.40536 89.80261 assigned negative charge : -461.3643 centred at (gu) : 94.07517 90.82665 90.25091 start vw surface at 0.1100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 194411 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28209 grid for indexing accessible points = 1.400000 m= 93165 mr = 138109 m= 33292 mr = 73684 m= 8217 mr = 25951 m= 1107 mr = 6143 m= 49 mr = 739 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 2692 time to turn everything in is 1.070000 number of dielectric boundary points 85604 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 23424 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) : 1.862769 object centre at (A) : 7.043499 80.67400 27.12600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8005832 -0.2523101 midg,1,midg; midg,igrid,midg -0.2455843 -0.3161572 1,midg,midg; igrid,midg,midg -0.1927160 -0.5634682 gauss-seidel spectral radius is 0.9992775 estimated iterations to convergence 294 setup time was (sec) 1.310000 now iterating at: 16:15:55 rms-change max change #iterations 10.74906 293.2413 at 10iterations 6.430999 137.2218 at 20iterations 3.810977 74.91217 at 30iterations 2.245280 46.52620 at 40iterations 1.318602 31.01737 at 50iterations 0.7717476 14.32183 at 60iterations 0.4521314 10.92723 at 70iterations 0.2638853 4.816254 at 80iterations 0.1537355 2.927691 at 90iterations 8.9523800E-02 1.598831 at 100iterations 5.1970091E-02 1.147610 at 110iterations 3.0219108E-02 0.5867677 at 120iterations 1.7579867E-02 0.2966499 at 130iterations 1.0185729E-02 0.2227230 at 140iterations 5.9090992E-03 0.1036911 at 150iterations 3.4271048E-03 6.0746193E-02 at 160iterations 1.9890652E-03 4.0126801E-02 at 170iterations 1.1523224E-03 1.9773483E-02 at 180iterations finished qdiffx linear iterations at : 16:16:06 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 1.1523224E-03 1.9773483E-02 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.88000 DelPhi exited at 16:16:07 12.881u 0.198s 0:13.34 97.9% 0+0k 0+0io 0pf+0w