Tue Oct 11 01:39:56 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 Tue Oct 11 2011 at 01:39:56 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 = 2689 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: 0.5933532 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): 18.17200 78.17000 ymin,ymax (A): -11.75100 44.12800 zmin,zma (A): -7.823000 35.17200 x,y,z range (A): 59.99800 55.87900 42.99500 scale (grids/A): 0.5933532 object centre (A): 48.17100 16.18850 13.67450 number of atom coordinates read : 2689 total number of charged atoms : 2548 net assigned charge : 8.500024 assigned positive charge : 407.4056 centred at (gu) : 88.40738 89.89448 89.91404 assigned negative charge : -398.9064 centred at (gu) : 88.67433 90.06535 90.03172 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6187 nv = 96 ne = 84 npr = 54171 no. pairs analyzed = 54171 no. exposed pairs = 3243 no. arc points = 23008 no. surface atoms = 1093 nbur = 1596 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 = 1.456000 m= 268 mr = 3383 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 42 time to turn everything in is 0.2100000 number of dielectric boundary points 3043 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2273 ## 251 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7771 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4379599E-09 -8.2585905E-10 midg,1,midg; midg,igrid,midg 8.0701685E-09 -2.4540301E-09 1,midg,midg; igrid,midg,midg 1.5426100E-08 -3.8290695E-09 gauss-seidel spectral radius is 0.9853072 estimated iterations to convergence 68 setup time was (sec) 0.4000000 now iterating at: 01:39:57 rms-change max change #iterations 0.1040520 18.93700 at 10iterations 9.3387151E-03 1.394825 at 20iterations 1.1480697E-03 0.2624741 at 30iterations 2.5165238E-04 5.9783936E-02 at 40iterations 5.9839924E-05 1.4957428E-02 at 50iterations finished qdiffx linear iterations at : 01:40:00 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 5.9839924E-05 1.4957428E-02 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 01:40:01 3.434u 0.183s 0:04.13 87.4% 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 Tue Oct 11 2011 at 01:40:01 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 = 2689 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: 1.780059 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): 18.17200 78.17000 ymin,ymax (A): -11.75100 44.12800 zmin,zma (A): -7.823000 35.17200 x,y,z range (A): 59.99800 55.87900 42.99500 scale (grids/A): 1.780059 object centre (A): 48.17100 16.18850 13.67450 number of atom coordinates read : 2689 total number of charged atoms : 2548 net assigned charge : 8.500024 assigned positive charge : 407.4056 centred at (gu) : 85.22153 89.68312 89.74152 assigned negative charge : -398.9064 centred at (gu) : 86.02282 90.19588 90.09490 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 67585 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23008 grid for indexing accessible points = 1.400000 m= 22257 mr = 46684 m= 2981 mr = 16169 m= 91 mr = 1822 m= 0 mr = 18 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 2941 time to turn everything in is 0.3300000 number of dielectric boundary points 28221 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 237 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 19867 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) : 0.5933532 object centre at (A) : 48.17100 16.18850 13.67450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3199657E-02 5.2126134E-03 midg,1,midg; midg,igrid,midg 2.9478835E-02 -2.3872783E-02 1,midg,midg; igrid,midg,midg 1.7080009E-02 1.5120542E-03 gauss-seidel spectral radius is 0.9984460 estimated iterations to convergence 201 setup time was (sec) 0.5400000 now iterating at: 01:40:01 rms-change max change #iterations 3.780331 175.0438 at 10iterations 1.681021 68.21744 at 20iterations 0.7464086 27.53764 at 30iterations 0.3303719 11.92526 at 40iterations 0.1475249 4.885915 at 50iterations 6.5787047E-02 2.263182 at 60iterations 2.9426664E-02 0.9465256 at 70iterations 1.3255763E-02 0.4512019 at 80iterations 6.0327277E-03 0.2402267 at 90iterations 2.7939810E-03 0.1044540 at 100iterations 1.3595958E-03 6.1424255E-02 at 110iterations 6.9647771E-04 2.8551102E-02 at 120iterations finished qdiffx linear iterations at : 01:40:08 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 6.9647771E-04 2.8551102E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 01:40:09 7.796u 0.208s 0:08.67 92.1% 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 Tue Oct 11 2011 at 01:40:09 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 = 2689 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: 2.670089 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): 18.17200 78.17000 ymin,ymax (A): -11.75100 44.12800 zmin,zma (A): -7.823000 35.17200 x,y,z range (A): 59.99800 55.87900 42.99500 scale (grids/A): 2.670089 object centre (A): 48.17100 16.18850 13.67450 number of atom coordinates read : 2689 total number of charged atoms : 2548 net assigned charge : 8.500024 assigned positive charge : 407.4056 centred at (gu) : 82.83229 89.52438 89.61218 assigned negative charge : -398.9064 centred at (gu) : 84.03405 90.29378 90.14227 start vw surface at 0.1100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 156668 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23008 grid for indexing accessible points = 1.400000 m= 74879 mr = 113668 m= 24628 mr = 60765 m= 5204 mr = 19556 m= 505 mr = 3906 m= 15 mr = 331 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 10193 time to turn everything in is 0.8400000 number of dielectric boundary points 63673 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 20377 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) : 1.780059 object centre at (A) : 48.17100 16.18850 13.67450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2551964 5.3527445E-02 midg,1,midg; midg,igrid,midg 0.3510294 -0.4518681 1,midg,midg; igrid,midg,midg 0.1361813 0.2185642 gauss-seidel spectral radius is 0.9992042 estimated iterations to convergence 280 setup time was (sec) 1.070000 now iterating at: 01:40:11 rms-change max change #iterations 9.051971 270.4744 at 10iterations 5.147668 154.7332 at 20iterations 2.907201 60.80749 at 30iterations 1.638923 34.78923 at 40iterations 0.9236098 20.35146 at 50iterations 0.5198112 11.03153 at 60iterations 0.2925531 5.793007 at 70iterations 0.1643492 3.088312 at 80iterations 9.2669435E-02 1.820866 at 90iterations 5.2168362E-02 1.033519 at 100iterations 2.9467233E-02 0.6672287 at 110iterations 1.6603205E-02 0.3555946 at 120iterations 9.4621722E-03 0.1835480 at 130iterations 5.3942236E-03 0.1075592 at 140iterations 3.1308418E-03 6.5910339E-02 at 150iterations 1.8669284E-03 4.3930054E-02 at 160iterations 1.1584803E-03 2.9941559E-02 at 170iterations 7.5193163E-04 1.9840240E-02 at 180iterations finished qdiffx linear iterations at : 01:40:22 total time elapsed so far: 12.16000 # loops : 180 mean,max change (kT/e) : 7.5193163E-04 1.9840240E-02 energy calculations done at 12.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.29000 DelPhi exited at 01:40:23 12.293u 0.207s 0:13.08 95.4% 0+0k 0+0io 0pf+0w