Tue Oct 11 07:08:17 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 Tue Oct 11 2011 at 07:08:18 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3449 !!! WARNING: UMP 1145 has a net charge of -0.1000 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: 0.3911486 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): -18.25000 57.93800 ymin,ymax (A): -26.72500 59.97300 zmin,zma (A): -34.67900 56.33500 x,y,z range (A): 76.18800 86.69800 91.01400 scale (grids/A): 0.3911486 object centre (A): 19.84400 16.62400 10.82800 number of atom coordinates read : 3449 total number of charged atoms : 3244 net assigned charge : 4.400015 assigned positive charge : 513.9623 centred at (gu) : 86.03433 85.39482 84.20276 assigned negative charge : -509.5639 centred at (gu) : 86.09753 85.33274 84.08859 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 2985 nv = 96 ne = 84 npr = 70333 no. pairs analyzed = 70333 no. exposed pairs = 4137 no. arc points = 28879 no. surface atoms = 1404 nbur = 2045 mkacc time = 0.1600000 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 = 2.128000 m= 69 mr = 1425 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 1629 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2119 ## 581 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 4126 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3458516E-12 4.5161303E-14 midg,1,midg; midg,igrid,midg -3.1049469E-13 4.3430320E-14 1,midg,midg; igrid,midg,midg 7.8665866E-13 -1.5657499E-14 gauss-seidel spectral radius is 0.9667214 estimated iterations to convergence 46 setup time was (sec) 0.5600000 now iterating at: 07:08:18 rms-change max change #iterations 1.4541161E-02 3.334084 at 10iterations 1.2981235E-03 0.3938046 at 20iterations 2.6018120E-04 7.9301834E-02 at 30iterations 5.3104493E-05 1.6260147E-02 at 40iterations 1.0838004E-05 3.3226013E-03 at 50iterations finished qdiffx linear iterations at : 07:08:21 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 1.0838004E-05 3.3226013E-03 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 07:08:21 3.237u 0.158s 0:03.70 91.3% 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 07:08:21 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3449 !!! WARNING: UMP 1145 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.173446 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): -18.25000 57.93800 ymin,ymax (A): -26.72500 59.97300 zmin,zma (A): -34.67900 56.33500 x,y,z range (A): 76.18800 86.69800 91.01400 scale (grids/A): 1.173446 object centre (A): 19.84400 16.62400 10.82800 number of atom coordinates read : 3449 total number of charged atoms : 3244 net assigned charge : 4.400015 assigned positive charge : 513.9623 centred at (gu) : 78.10210 76.18327 72.60716 assigned negative charge : -509.5639 centred at (gu) : 78.29225 75.99810 72.26550 start vw surface at 0.1800000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 35951 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28879 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.988000 m= 7216 mr = 23648 m= 248 mr = 4359 m= 1 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 667 time to turn everything in is 0.3600000 number of dielectric boundary points 15362 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 681 ## 46 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 21184 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) : 0.3911486 object centre at (A) : 19.84400 16.62400 10.82800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.9792134E-03 -1.1823637E-06 midg,1,midg; midg,igrid,midg -3.7715374E-03 9.0553563E-05 1,midg,midg; igrid,midg,midg 3.6315648E-03 2.0054572E-04 gauss-seidel spectral radius is 0.9963175 estimated iterations to convergence 132 setup time was (sec) 0.6300000 now iterating at: 07:08:22 rms-change max change #iterations 1.538507 102.8565 at 10iterations 0.4461594 26.90213 at 20iterations 0.1291434 7.208607 at 30iterations 3.7529800E-02 1.971976 at 40iterations 1.1213183E-02 0.6037374 at 50iterations 3.6627543E-03 0.2510529 at 60iterations 1.5172069E-03 9.2502594E-02 at 70iterations 7.9189235E-04 5.0590515E-02 at 80iterations 4.7055559E-04 3.0464172E-02 at 90iterations 2.9014019E-04 1.8795013E-02 at 100iterations 1.7986447E-04 1.1583328E-02 at 110iterations 1.1162949E-04 7.1964264E-03 at 120iterations finished qdiffx linear iterations at : 07:08:28 total time elapsed so far: 6.500000 # loops : 120 mean,max change (kT/e) : 1.1162949E-04 7.1964264E-03 energy calculations done at 6.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.680000 DelPhi exited at 07:08:28 6.682u 0.185s 0:07.16 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 Tue Oct 11 2011 at 07:08:28 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3449 !!! WARNING: UMP 1145 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.760169 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): -18.25000 57.93800 ymin,ymax (A): -26.72500 59.97300 zmin,zma (A): -34.67900 56.33500 x,y,z range (A): 76.18800 86.69800 91.01400 scale (grids/A): 1.760169 object centre (A): 19.84400 16.62400 10.82800 number of atom coordinates read : 3449 total number of charged atoms : 3244 net assigned charge : 4.400015 assigned positive charge : 513.9623 centred at (gu) : 72.15293 69.27467 63.91054 assigned negative charge : -509.5639 centred at (gu) : 72.43821 68.99702 63.39806 start vw surface at 0.1900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 84981 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28879 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.960000 m= 29961 mr = 59502 m= 4197 mr = 22441 m= 151 mr = 2591 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 2121 time to turn everything in is 0.7100000 number of dielectric boundary points 34732 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 265 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 25248 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) : 1.173446 object centre at (A) : 19.84400 16.62400 10.82800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2972174 2.3508345E-04 midg,1,midg; midg,igrid,midg -0.1130614 2.9513279E-03 1,midg,midg; igrid,midg,midg 9.9332631E-02 7.0381146E-03 gauss-seidel spectral radius is 0.9983565 estimated iterations to convergence 196 setup time was (sec) 0.9700000 now iterating at: 07:08:30 rms-change max change #iterations 4.772751 210.4298 at 10iterations 2.097644 69.88422 at 20iterations 0.9266816 33.21825 at 30iterations 0.4067149 12.77829 at 40iterations 0.1781527 5.571659 at 50iterations 7.8110710E-02 2.671703 at 60iterations 3.4216307E-02 1.053071 at 70iterations 1.4995197E-02 0.5642414 at 80iterations 6.5980526E-03 0.2184105 at 90iterations 2.9371830E-03 9.4371796E-02 at 100iterations 1.3497276E-03 4.5363426E-02 at 110iterations 6.5823179E-04 2.3796082E-02 at 120iterations 3.5805002E-04 1.3980865E-02 at 130iterations 2.2177486E-04 8.2855225E-03 at 140iterations 1.5037268E-04 5.4721832E-03 at 150iterations 1.0645055E-04 3.8394928E-03 at 160iterations 7.6744567E-05 2.7332306E-03 at 170iterations 5.5774828E-05 1.9912720E-03 at 180iterations finished qdiffx linear iterations at : 07:08:39 total time elapsed so far: 10.61000 # loops : 180 mean,max change (kT/e) : 5.5774828E-05 1.9912720E-03 energy calculations done at 10.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.79000 DelPhi exited at 07:08:40 10.794u 0.178s 0:11.39 96.2% 0+0k 0+0io 0pf+0w