Sun Oct 9 07:43:51 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 07:43:51 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 = 2551 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: 0.5482068 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): -4.422000 42.15300 ymin,ymax (A): 35.68900 88.95300 zmin,zma (A): -3.138000 61.80100 x,y,z range (A): 46.57500 53.26399 64.93900 scale (grids/A): 0.5482068 object centre (A): 18.86550 62.32100 29.33150 number of atom coordinates read : 2551 total number of charged atoms : 2406 net assigned charge : -12.49998 assigned positive charge : 380.2139 centred at (gu) : 90.61588 88.81002 89.74133 assigned negative charge : -392.7143 centred at (gu) : 90.77632 88.48484 89.70585 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5127 nv = 96 ne = 84 npr = 50914 no. pairs analyzed = 50914 no. exposed pairs = 3606 no. arc points = 25596 no. surface atoms = 1201 nbur = 1350 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 = 1.568000 m= 195 mr = 2399 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2917 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2601 ## 325 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6577 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1007303E-09 -5.4863492E-10 midg,1,midg; midg,igrid,midg -3.9868087E-09 8.6801583E-10 1,midg,midg; igrid,midg,midg 1.5988730E-10 -2.1514610E-09 gauss-seidel spectral radius is 0.9828196 estimated iterations to convergence 63 setup time was (sec) 0.5300000 now iterating at: 07:43:51 rms-change max change #iterations 6.6477351E-02 12.52583 at 10iterations 4.4387756E-03 0.8505135 at 20iterations 2.9689775E-04 5.2883148E-02 at 30iterations 2.0633681E-05 3.2348633E-03 at 40iterations 1.8348398E-06 3.3569336E-04 at 50iterations finished qdiffx linear iterations at : 07:43:54 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 1.8348398E-06 3.3569336E-04 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 07:43:55 3.505u 0.213s 0:04.00 92.7% 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 07:43:55 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 = 2551 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: 1.644620 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): -4.422000 42.15300 ymin,ymax (A): 35.68900 88.95300 zmin,zma (A): -3.138000 61.80100 x,y,z range (A): 46.57500 53.26399 64.93900 scale (grids/A): 1.644620 object centre (A): 18.86550 62.32100 29.33150 number of atom coordinates read : 2551 total number of charged atoms : 2406 net assigned charge : -12.49998 assigned positive charge : 380.2139 centred at (gu) : 91.84735 86.42942 89.22363 assigned negative charge : -392.7143 centred at (gu) : 92.32870 85.45419 89.11694 start vw surface at 0.1400000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 55923 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25596 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 16759 mr = 35543 m= 1531 mr = 11105 m= 31 mr = 700 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 155 time to turn everything in is 0.4100000 number of dielectric boundary points 26896 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 287 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 18463 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) : 0.5482068 object centre at (A) : 18.86550 62.32100 29.33150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6101121E-02 -4.8494427E-03 midg,1,midg; midg,igrid,midg -2.6538776E-02 3.9391266E-03 1,midg,midg; igrid,midg,midg -3.4078129E-03 -1.6463626E-02 gauss-seidel spectral radius is 0.9981683 estimated iterations to convergence 186 setup time was (sec) 0.6800000 now iterating at: 07:43:56 rms-change max change #iterations 3.103897 210.6861 at 10iterations 1.288175 54.50653 at 20iterations 0.5312716 21.04571 at 30iterations 0.2200746 8.753476 at 40iterations 9.1484182E-02 4.186391 at 50iterations 3.7967775E-02 1.532632 at 60iterations 1.5703963E-02 0.6461706 at 70iterations 6.5059527E-03 0.2821202 at 80iterations 2.6932382E-03 0.1082029 at 90iterations 1.1179412E-03 4.2213440E-02 at 100iterations 4.6312236E-04 1.7635345E-02 at 110iterations 1.9255943E-04 7.3680878E-03 at 120iterations finished qdiffx linear iterations at : 07:44:02 total time elapsed so far: 7.270000 # loops : 120 mean,max change (kT/e) : 1.9255943E-04 7.3680878E-03 energy calculations done at 7.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.440000 DelPhi exited at 07:44:03 7.447u 0.164s 0:07.93 95.8% 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 07:44:03 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 = 2551 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: 2.466931 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): -4.422000 42.15300 ymin,ymax (A): 35.68900 88.95300 zmin,zma (A): -3.138000 61.80100 x,y,z range (A): 46.57500 53.26399 64.93900 scale (grids/A): 2.466931 object centre (A): 18.86550 62.32100 29.33150 number of atom coordinates read : 2551 total number of charged atoms : 2406 net assigned charge : -12.49998 assigned positive charge : 380.2139 centred at (gu) : 92.77081 84.64408 88.83537 assigned negative charge : -392.7143 centred at (gu) : 93.49286 83.18125 88.67534 start vw surface at 0.1400000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 129185 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25596 grid for indexing accessible points = 1.400000 m= 58578 mr = 87009 m= 15695 mr = 45392 m= 2170 mr = 11366 m= 156 mr = 1330 m= 1 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 484 time to turn everything in is 0.9700000 number of dielectric boundary points 60609 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 19225 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) : 1.644620 object centre at (A) : 18.86550 62.32100 29.33150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9034436 -7.7606030E-02 midg,1,midg; midg,igrid,midg -0.3491529 7.3873840E-02 1,midg,midg; igrid,midg,midg -4.6478301E-02 -0.2075860 gauss-seidel spectral radius is 0.9991279 estimated iterations to convergence 268 setup time was (sec) 1.290000 now iterating at: 07:44:04 rms-change max change #iterations 8.198993 298.9161 at 10iterations 4.579835 135.2907 at 20iterations 2.568376 73.65378 at 30iterations 1.424726 34.72397 at 40iterations 0.7909595 19.44702 at 50iterations 0.4372280 10.04424 at 60iterations 0.2413218 5.425178 at 70iterations 0.1329105 3.162708 at 80iterations 7.3118210E-02 2.031237 at 90iterations 4.0116962E-02 0.9216881 at 100iterations 2.2069359E-02 0.5220633 at 110iterations 1.2121617E-02 0.3212166 at 120iterations 6.6423626E-03 0.1616096 at 130iterations 3.6365425E-03 8.0718458E-02 at 140iterations 1.9917579E-03 4.2684555E-02 at 150iterations 1.0958074E-03 2.3782253E-02 at 160iterations 5.9904851E-04 1.3805389E-02 at 170iterations 3.2884171E-04 7.6007843E-03 at 180iterations finished qdiffx linear iterations at : 07:44:15 total time elapsed so far: 11.98000 # loops : 180 mean,max change (kT/e) : 3.2884171E-04 7.6007843E-03 energy calculations done at 11.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.15000 DelPhi exited at 07:44:15 12.150u 0.247s 0:12.70 97.5% 0+0k 0+0io 0pf+0w