Wed Dec 28 11:04:46 PST 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 Wed Dec 28 2011 at 11:04:46 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 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: 0.6023790 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): -24.13800 34.96100 ymin,ymax (A): -18.87800 20.70500 zmin,zma (A): -2.896000 38.70800 x,y,z range (A): 59.09900 39.58300 41.60400 scale (grids/A): 0.6023790 object centre (A): 5.411501 0.9134998 17.90600 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 2.000006 assigned positive charge : 292.2239 centred at (gu) : 89.71742 90.15799 90.35211 assigned negative charge : -290.2242 centred at (gu) : 89.72469 90.27128 90.50413 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 4852 nv = 96 ne = 84 npr = 39847 no. pairs analyzed = 39847 no. exposed pairs = 2439 no. arc points = 16874 no. surface atoms = 837 nbur = 1125 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 183 mr = 2640 m= 0 mr = 11 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.2500000 number of dielectric boundary points 2384 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1747 ## 187 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 5882 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9312261E-09 -3.8991939E-09 midg,1,midg; midg,igrid,midg 4.0899151E-09 -2.5089462E-09 1,midg,midg; igrid,midg,midg 1.2431751E-09 6.9728040E-10 gauss-seidel spectral radius is 0.9856814 estimated iterations to convergence 69 setup time was (sec) 0.5000000 now iterating at: 11:04:47 rms-change max change #iterations 9.7207181E-02 16.72609 at 10iterations 8.3271274E-03 1.374954 at 20iterations 7.0390938E-04 0.1197138 at 30iterations 6.1132108E-05 9.9029541E-03 at 40iterations 5.0438503E-06 8.3971024E-04 at 50iterations finished qdiffx linear iterations at : 11:04:50 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 5.0438503E-06 8.3971024E-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) 3.470000 DelPhi exited at 11:04:50 3.475u 0.203s 0:03.99 91.9% 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 Wed Dec 28 2011 at 11:04:50 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.807137 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): -24.13800 34.96100 ymin,ymax (A): -18.87800 20.70500 zmin,zma (A): -2.896000 38.70800 x,y,z range (A): 59.09900 39.58300 41.60400 scale (grids/A): 1.807137 object centre (A): 5.411501 0.9134998 17.90600 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 2.000006 assigned positive charge : 292.2239 centred at (gu) : 89.15232 90.47384 91.05673 assigned negative charge : -290.2242 centred at (gu) : 89.17408 90.81398 91.51250 start vw surface at 0.1800000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 52537 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16874 grid for indexing accessible points = 1.400000 m= 18617 mr = 36173 m= 2239 mr = 14017 m= 61 mr = 1287 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 245 time to turn everything in is 0.4600000 number of dielectric boundary points 21977 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 14321 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) : 0.6023790 object centre at (A) : 5.411501 0.9134998 17.90600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.1254516E-03 -7.8033078E-03 midg,1,midg; midg,igrid,midg 2.7555767E-03 -5.9979218E-03 1,midg,midg; igrid,midg,midg 3.8650163E-02 3.1705014E-02 gauss-seidel spectral radius is 0.9984075 estimated iterations to convergence 199 setup time was (sec) 0.8200000 now iterating at: 11:04:51 rms-change max change #iterations 3.269551 157.1293 at 10iterations 1.432829 57.24033 at 20iterations 0.6335360 23.91988 at 30iterations 0.2789297 10.60080 at 40iterations 0.1230229 4.512182 at 50iterations 5.4100059E-02 2.274834 at 60iterations 2.3780275E-02 0.9436293 at 70iterations 1.0481107E-02 0.4150620 at 80iterations 4.6257158E-03 0.1672201 at 90iterations 2.0362691E-03 7.5489044E-02 at 100iterations 9.0005330E-04 3.4357548E-02 at 110iterations 3.9643035E-04 1.5941620E-02 at 120iterations finished qdiffx linear iterations at : 11:04:58 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 3.9643035E-04 1.5941620E-02 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 11:04:59 7.679u 0.301s 0:08.57 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 Wed Dec 28 2011 at 11:04:59 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 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: 2.710706 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): -24.13800 34.96100 ymin,ymax (A): -18.87800 20.70500 zmin,zma (A): -2.896000 38.70800 x,y,z range (A): 59.09900 39.58300 41.60400 scale (grids/A): 2.710706 object centre (A): 5.411501 0.9134998 17.90600 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 2.000006 assigned positive charge : 292.2239 centred at (gu) : 88.72849 90.71083 91.58495 assigned negative charge : -290.2242 centred at (gu) : 88.76109 91.22103 92.26886 start vw surface at 0.1300000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 121349 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16874 grid for indexing accessible points = 1.400000 m= 61911 mr = 87556 m= 20456 mr = 51239 m= 3644 mr = 16493 m= 254 mr = 2566 m= 4 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 807 time to turn everything in is 1.050000 number of dielectric boundary points 49656 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 14639 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) : 1.807137 object centre at (A) : 5.411501 0.9134998 17.90600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.8363158E-02 -6.6611543E-02 midg,1,midg; midg,igrid,midg 1.7540777E-02 -5.3200431E-02 1,midg,midg; igrid,midg,midg 0.4370341 0.3168812 gauss-seidel spectral radius is 0.9991763 estimated iterations to convergence 275 setup time was (sec) 1.410000 now iterating at: 11:05:01 rms-change max change #iterations 8.003511 372.4326 at 10iterations 4.544284 168.0679 at 20iterations 2.565362 68.21532 at 30iterations 1.435838 35.56946 at 40iterations 0.8023449 17.76211 at 50iterations 0.4475643 9.701484 at 60iterations 0.2492088 5.570208 at 70iterations 0.1392743 2.931433 at 80iterations 7.7417128E-02 1.657206 at 90iterations 4.3097857E-02 0.9337616 at 100iterations 2.3985023E-02 0.5561383 at 110iterations 1.3347578E-02 0.2755804 at 120iterations 7.4135321E-03 0.1672888 at 130iterations 4.1329204E-03 0.1054459 at 140iterations 2.2994052E-03 5.0882339E-02 at 150iterations 1.2780122E-03 2.7748108E-02 at 160iterations 7.1033201E-04 1.5430450E-02 at 170iterations 3.9531323E-04 8.6510777E-03 at 180iterations finished qdiffx linear iterations at : 11:05:13 total time elapsed so far: 13.65000 # loops : 180 mean,max change (kT/e) : 3.9531323E-04 8.6510777E-03 energy calculations done at 13.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.84000 DelPhi exited at 11:05:14 13.843u 0.366s 0:14.88 95.4% 0+0k 0+0io 0pf+0w