Mon Oct 10 16:26:37 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 Mon Oct 10 2011 at 16:26:37 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3035 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5623302 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): -20.79500 38.45100 ymin,ymax (A): 25.14100 81.04900 zmin,zma (A): -18.47200 44.83600 x,y,z range (A): 59.24600 55.90800 63.30800 scale (grids/A): 0.5623302 object centre (A): 8.828000 53.09500 13.18200 number of atom coordinates read : 3035 total number of charged atoms : 2888 net assigned charge : 13.50003 assigned positive charge : 461.6299 centred at (gu) : 89.71821 89.89141 91.89394 assigned negative charge : -448.1313 centred at (gu) : 89.75417 89.99889 91.86172 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6739 nv = 96 ne = 84 npr = 55106 no. pairs analyzed = 55106 no. exposed pairs = 4475 no. arc points = 34202 no. surface atoms = 1466 nbur = 1569 mkacc time = 9.0000004E-02 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= 274 mr = 3005 m= 0 mr = 11 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3997 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3393 ## 442 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8416 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5332374E-10 3.0421288E-09 midg,1,midg; midg,igrid,midg 2.9049578E-09 2.2851297E-10 1,midg,midg; igrid,midg,midg 2.1178836E-09 1.0429382E-09 gauss-seidel spectral radius is 0.9837202 estimated iterations to convergence 64 setup time was (sec) 0.4100000 now iterating at: 16:26:37 rms-change max change #iterations 8.7062135E-02 14.64973 at 10iterations 6.2202830E-03 0.9862576 at 20iterations 4.5233613E-04 8.4858894E-02 at 30iterations 3.6985948E-05 5.7640076E-03 at 40iterations 4.3318082E-06 6.6661835E-04 at 50iterations finished qdiffx linear iterations at : 16:26:40 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 4.3318082E-06 6.6661835E-04 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 16:26:41 3.438u 0.169s 0:03.91 91.8% 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 Mon Oct 10 2011 at 16:26:41 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3035 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.686991 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): -20.79500 38.45100 ymin,ymax (A): 25.14100 81.04900 zmin,zma (A): -18.47200 44.83600 x,y,z range (A): 59.24600 55.90800 63.30800 scale (grids/A): 1.686991 object centre (A): 8.828000 53.09500 13.18200 number of atom coordinates read : 3035 total number of charged atoms : 2888 net assigned charge : 13.50003 assigned positive charge : 461.6299 centred at (gu) : 89.15363 89.67363 95.68115 assigned negative charge : -448.1313 centred at (gu) : 89.26228 89.99638 95.58475 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 72513 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34202 grid for indexing accessible points = 1.400000 m= 22718 mr = 44435 m= 2604 mr = 15144 m= 105 mr = 1140 m= 2 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 203 time to turn everything in is 0.3700000 number of dielectric boundary points 37219 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 342 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 22227 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) : 0.5623302 object centre at (A) : 8.828000 53.09500 13.18200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2637299E-02 2.4560893E-02 midg,1,midg; midg,igrid,midg 1.8826995E-02 1.4450639E-02 1,midg,midg; igrid,midg,midg 1.3479819E-02 1.9105857E-02 gauss-seidel spectral radius is 0.9983456 estimated iterations to convergence 195 setup time was (sec) 0.5900000 now iterating at: 16:26:41 rms-change max change #iterations 3.620094 160.8322 at 10iterations 1.547056 69.56355 at 20iterations 0.6688636 24.14758 at 30iterations 0.2867710 10.74061 at 40iterations 0.1238816 4.229084 at 50iterations 5.3793766E-02 1.864413 at 60iterations 2.3160763E-02 0.8033981 at 70iterations 9.9932300E-03 0.3810396 at 80iterations 4.3282676E-03 0.1460112 at 90iterations 1.8699470E-03 8.3347321E-02 at 100iterations 8.1190455E-04 2.7511597E-02 at 110iterations 3.5124866E-04 1.2493134E-02 at 120iterations finished qdiffx linear iterations at : 16:26:49 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 3.5124866E-04 1.2493134E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 16:26:49 7.876u 0.188s 0:08.56 94.0% 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 Mon Oct 10 2011 at 16:26:49 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3035 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.530486 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): -20.79500 38.45100 ymin,ymax (A): 25.14100 81.04900 zmin,zma (A): -18.47200 44.83600 x,y,z range (A): 59.24600 55.90800 63.30800 scale (grids/A): 2.530486 object centre (A): 8.828000 53.09500 13.18200 number of atom coordinates read : 3035 total number of charged atoms : 2888 net assigned charge : 13.50003 assigned positive charge : 461.6299 centred at (gu) : 88.73042 89.51024 98.52145 assigned negative charge : -448.1313 centred at (gu) : 88.89333 89.99453 98.37703 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 167384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34202 grid for indexing accessible points = 1.400000 m= 76040 mr = 109290 m= 23423 mr = 58499 m= 4035 mr = 16921 m= 341 mr = 2419 m= 9 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 632 time to turn everything in is 0.8800000 number of dielectric boundary points 83996 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 23089 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) : 1.686991 object centre at (A) : 8.828000 53.09500 13.18200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6817862 0.3162696 midg,1,midg; midg,igrid,midg 0.2504544 0.1843960 1,midg,midg; igrid,midg,midg 1.6907843E-02 0.1847056 gauss-seidel spectral radius is 0.9992016 estimated iterations to convergence 279 setup time was (sec) 1.120000 now iterating at: 16:26:51 rms-change max change #iterations 9.325908 283.0520 at 10iterations 5.415555 125.9077 at 20iterations 3.115782 75.78566 at 30iterations 1.780581 38.74993 at 40iterations 1.014267 23.00853 at 50iterations 0.5773337 14.49572 at 60iterations 0.3272447 7.209816 at 70iterations 0.1852266 4.008553 at 80iterations 0.1045706 2.216480 at 90iterations 5.9037875E-02 1.229174 at 100iterations 3.3248704E-02 0.7424088 at 110iterations 1.8718394E-02 0.4321527 at 120iterations 1.0539779E-02 0.2233667 at 130iterations 5.9309853E-03 0.1126041 at 140iterations 3.3373919E-03 6.3270569E-02 at 150iterations 1.8737316E-03 3.6788881E-02 at 160iterations 1.0536768E-03 2.0198345E-02 at 170iterations 5.9340888E-04 1.1123657E-02 at 180iterations finished qdiffx linear iterations at : 16:27:02 total time elapsed so far: 12.63000 # loops : 180 mean,max change (kT/e) : 5.9340888E-04 1.1123657E-02 energy calculations done at 12.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.76000 DelPhi exited at 16:27:03 12.759u 0.208s 0:13.28 97.5% 0+0k 0+0io 0pf+0w