Sun Oct 9 11:36:32 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 11:36:32 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2032 !!! WARNING: HIR 203 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6512156 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): 28.10400 75.28000 ymin,ymax (A): 11.56500 66.23200 zmin,zma (A): 57.51800 99.00900 x,y,z range (A): 47.17600 54.66700 41.49100 scale (grids/A): 0.6512156 object centre (A): 51.69200 38.89850 78.26350 number of atom coordinates read : 2032 total number of charged atoms : 1968 net assigned charge : -0.4859942 assigned positive charge : 302.5347 centred at (gu) : 89.13342 90.08832 89.25686 assigned negative charge : -303.0213 centred at (gu) : 89.04186 90.04942 89.33933 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6153 nv = 96 ne = 84 npr = 39221 no. pairs analyzed = 39221 no. exposed pairs = 2860 no. arc points = 19580 no. surface atoms = 961 nbur = 1071 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 353 mr = 3214 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3253 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1934 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7216 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0698785E-08 -9.5285344E-09 midg,1,midg; midg,igrid,midg -5.6325593E-09 3.8946282E-09 1,midg,midg; igrid,midg,midg -1.4822864E-08 8.4666736E-09 gauss-seidel spectral radius is 0.9877404 estimated iterations to convergence 74 setup time was (sec) 0.3600000 now iterating at: 11:36:33 rms-change max change #iterations 0.1359700 21.05943 at 10iterations 1.3536450E-02 1.981098 at 20iterations 1.4101849E-03 0.3349447 at 30iterations 1.4105676E-04 2.1633148E-02 at 40iterations 1.4713623E-05 2.3880005E-03 at 50iterations finished qdiffx linear iterations at : 11:36:36 total time elapsed so far: 3.540000 # loops : 50 mean,max change (kT/e) : 1.4713623E-05 2.3880005E-03 energy calculations done at 3.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.700000 DelPhi exited at 11:36:37 3.709u 0.234s 0:04.41 89.1% 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 11:36:37 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2032 !!! WARNING: HIR 203 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.953647 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): 28.10400 75.28000 ymin,ymax (A): 11.56500 66.23200 zmin,zma (A): 57.51800 99.00900 x,y,z range (A): 47.17600 54.66700 41.49100 scale (grids/A): 1.953647 object centre (A): 51.69200 38.89850 78.26350 number of atom coordinates read : 2032 total number of charged atoms : 1968 net assigned charge : -0.4859942 assigned positive charge : 302.5347 centred at (gu) : 87.40004 90.26460 87.77031 assigned negative charge : -303.0213 centred at (gu) : 87.12547 90.14838 88.01807 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 65842 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19580 grid for indexing accessible points = 1.400000 m= 24552 mr = 44864 m= 4369 mr = 17589 m= 306 mr = 2749 m= 4 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 29788 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 15556 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) : 0.6512156 object centre at (A) : 51.69200 38.89850 78.26350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0568902E-02 -5.0798822E-03 midg,1,midg; midg,igrid,midg -1.9374151E-02 -2.1846704E-02 1,midg,midg; igrid,midg,midg -9.6795829E-03 1.4075219E-02 gauss-seidel spectral radius is 0.9986600 estimated iterations to convergence 216 setup time was (sec) 0.5700000 now iterating at: 11:36:37 rms-change max change #iterations 3.858046 166.6249 at 10iterations 1.814965 81.30858 at 20iterations 0.8525016 28.85437 at 30iterations 0.4032859 12.84419 at 40iterations 0.1905051 7.175000 at 50iterations 8.9507468E-02 3.047625 at 60iterations 4.2201549E-02 1.419840 at 70iterations 1.9916195E-02 0.7033029 at 80iterations 9.3567353E-03 0.3088255 at 90iterations 4.4436194E-03 0.1523743 at 100iterations 2.0823104E-03 7.0210099E-02 at 110iterations 9.8456512E-04 3.4337997E-02 at 120iterations finished qdiffx linear iterations at : 11:36:45 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 9.8456512E-04 3.4337997E-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) 7.830000 DelPhi exited at 11:36:45 7.837u 0.254s 0:08.44 95.7% 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 11:36:45 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2032 !!! WARNING: HIR 203 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.930470 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): 28.10400 75.28000 ymin,ymax (A): 11.56500 66.23200 zmin,zma (A): 57.51800 99.00900 x,y,z range (A): 47.17600 54.66700 41.49100 scale (grids/A): 2.930470 object centre (A): 51.69200 38.89850 78.26350 number of atom coordinates read : 2032 total number of charged atoms : 1968 net assigned charge : -0.4859942 assigned positive charge : 302.5347 centred at (gu) : 86.09991 90.39696 86.65540 assigned negative charge : -303.0213 centred at (gu) : 85.68832 90.22269 87.02717 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 152384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19580 grid for indexing accessible points = 1.400000 m= 76646 mr = 108947 m= 29996 mr = 61559 m= 8103 mr = 23941 m= 1216 mr = 5992 m= 65 mr = 782 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8800000 number of dielectric boundary points 67170 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 15744 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) : 1.953647 object centre at (A) : 51.69200 38.89850 78.26350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1420877 -7.9425387E-03 midg,1,midg; midg,igrid,midg -0.1689470 -0.4003352 1,midg,midg; igrid,midg,midg -0.1844012 8.9516632E-02 gauss-seidel spectral radius is 0.9992663 estimated iterations to convergence 291 setup time was (sec) 1.100000 now iterating at: 11:36:47 rms-change max change #iterations 9.218358 406.5461 at 10iterations 5.446755 140.5643 at 20iterations 3.199020 73.13191 at 30iterations 1.871897 42.83490 at 40iterations 1.091746 23.55941 at 50iterations 0.6353254 13.72260 at 60iterations 0.3694650 7.680348 at 70iterations 0.2138493 4.142175 at 80iterations 0.1238131 2.317833 at 90iterations 7.1499884E-02 1.467720 at 100iterations 4.1377325E-02 0.8567734 at 110iterations 2.3899412E-02 0.4848442 at 120iterations 1.3786116E-02 0.2614360 at 130iterations 7.9664141E-03 0.1656880 at 140iterations 4.6017212E-03 8.6324215E-02 at 150iterations 2.6447570E-03 4.6136856E-02 at 160iterations 1.5263817E-03 2.9222488E-02 at 170iterations 8.7889039E-04 1.7409801E-02 at 180iterations finished qdiffx linear iterations at : 11:36:59 total time elapsed so far: 12.72000 # loops : 180 mean,max change (kT/e) : 8.7889039E-04 1.7409801E-02 energy calculations done at 12.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.86000 DelPhi exited at 11:37:00 12.858u 1.364s 0:14.54 97.7% 0+0k 0+0io 0pf+0w