Mon Oct 10 16:59:21 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 16:59:21 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2868 !!! WARNING: GLM 103 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5667797 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): -34.62800 19.36800 ymin,ymax (A): -13.95800 29.88100 zmin,zma (A): 10.73200 73.54300 x,y,z range (A): 53.99600 43.83900 62.81100 scale (grids/A): 0.5667797 object centre (A): -7.630001 7.961501 42.13750 number of atom coordinates read : 2868 total number of charged atoms : 2723 net assigned charge : 1.406024 assigned positive charge : 427.2175 centred at (gu) : 89.99704 90.40282 89.95461 assigned negative charge : -425.8124 centred at (gu) : 90.01016 90.27670 89.93017 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 5993 nv = 96 ne = 84 npr = 58146 no. pairs analyzed = 58146 no. exposed pairs = 3512 no. arc points = 24884 no. surface atoms = 1195 nbur = 1673 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 = 1.512000 m= 224 mr = 3149 m= 0 mr = 28 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3040 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2500 ## 286 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 7705 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4655994E-10 5.0865018E-10 midg,1,midg; midg,igrid,midg -1.3963606E-09 2.0510720E-09 1,midg,midg; igrid,midg,midg 3.6252978E-10 8.4964787E-12 gauss-seidel spectral radius is 0.9839290 estimated iterations to convergence 65 setup time was (sec) 0.6600000 now iterating at: 16:59:22 rms-change max change #iterations 8.8471904E-02 16.97894 at 10iterations 6.5677846E-03 0.9743614 at 20iterations 4.9386342E-04 8.6391449E-02 at 30iterations 4.2748339E-05 7.7552795E-03 at 40iterations 6.0566153E-06 1.5907288E-03 at 50iterations finished qdiffx linear iterations at : 16:59:25 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 6.0566153E-06 1.5907288E-03 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.250000 DelPhi exited at 16:59:26 4.253u 0.230s 0:04.79 93.5% 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 16:59:26 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2868 !!! WARNING: GLM 103 has a net charge of -0.0940 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: 1.700339 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): -34.62800 19.36800 ymin,ymax (A): -13.95800 29.88100 zmin,zma (A): 10.73200 73.54300 x,y,z range (A): 53.99600 43.83900 62.81100 scale (grids/A): 1.700339 object centre (A): -7.630001 7.961501 42.13750 number of atom coordinates read : 2868 total number of charged atoms : 2723 net assigned charge : 1.406024 assigned positive charge : 427.2175 centred at (gu) : 89.99026 91.20772 89.86289 assigned negative charge : -425.8124 centred at (gu) : 90.03037 90.82987 89.79028 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 65603 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24884 grid for indexing accessible points = 1.400000 m= 20724 mr = 44555 m= 2457 mr = 14659 m= 93 mr = 1457 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 3252 time to turn everything in is 0.5600000 number of dielectric boundary points 28180 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 257 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 21061 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) : 0.5667797 object centre at (A) : -7.630001 7.961501 42.13750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3677149E-02 1.8939017E-03 midg,1,midg; midg,igrid,midg -2.3103706E-03 1.1994513E-02 1,midg,midg; igrid,midg,midg 5.1279739E-03 -1.2565937E-03 gauss-seidel spectral radius is 0.9983193 estimated iterations to convergence 194 setup time was (sec) 0.9000000 now iterating at: 16:59:27 rms-change max change #iterations 3.557967 167.5229 at 10iterations 1.525703 65.39577 at 20iterations 0.6537899 25.68199 at 30iterations 0.2819222 10.86616 at 40iterations 0.1213515 4.163254 at 50iterations 5.2579295E-02 1.848011 at 60iterations 2.2513416E-02 0.8386655 at 70iterations 9.7079668E-03 0.3857422 at 80iterations 4.2044930E-03 0.1444855 at 90iterations 1.8100635E-03 6.0168266E-02 at 100iterations 7.8218977E-04 3.4839630E-02 at 110iterations 3.3866431E-04 1.2369156E-02 at 120iterations finished qdiffx linear iterations at : 16:59:36 total time elapsed so far: 9.730000 # loops : 120 mean,max change (kT/e) : 3.3866431E-04 1.2369156E-02 energy calculations done at 9.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.900000 DelPhi exited at 16:59:37 9.907u 0.291s 0:10.77 94.6% 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 16:59:37 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2868 !!! WARNING: GLM 103 has a net charge of -0.0940 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: 2.550509 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): -34.62800 19.36800 ymin,ymax (A): -13.95800 29.88100 zmin,zma (A): 10.73200 73.54300 x,y,z range (A): 53.99600 43.83900 62.81100 scale (grids/A): 2.550509 object centre (A): -7.630001 7.961501 42.13750 number of atom coordinates read : 2868 total number of charged atoms : 2723 net assigned charge : 1.406024 assigned positive charge : 427.2175 centred at (gu) : 89.98521 91.81140 89.79414 assigned negative charge : -425.8124 centred at (gu) : 90.04552 91.24476 89.68533 start vw surface at 0.1700000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 152326 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24884 grid for indexing accessible points = 1.400000 m= 70639 mr = 108798 m= 21647 mr = 56774 m= 4120 mr = 16642 m= 422 mr = 3049 m= 9 mr = 243 m= 0 mr = 3 time to grow re-entrant surface = 0.7400001 no. cavity mid-points inaccessible to solvent = 10688 time to turn everything in is 1.340000 number of dielectric boundary points 63654 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 21775 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) : 1.700339 object centre at (A) : -7.630001 7.961501 42.13750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2463437 8.5012510E-02 midg,1,midg; midg,igrid,midg -3.0187905E-02 0.1310217 1,midg,midg; igrid,midg,midg 4.5245100E-02 5.5042122E-02 gauss-seidel spectral radius is 0.9991763 estimated iterations to convergence 275 setup time was (sec) 1.750000 now iterating at: 16:59:39 rms-change max change #iterations 8.891725 343.9214 at 10iterations 5.013025 142.8469 at 20iterations 2.810442 67.54515 at 30iterations 1.575977 36.09378 at 40iterations 0.8811834 18.42201 at 50iterations 0.4926408 10.01359 at 60iterations 0.2750616 5.679115 at 70iterations 0.1534602 3.081192 at 80iterations 8.5229449E-02 1.726475 at 90iterations 4.7515150E-02 1.070249 at 100iterations 2.6488945E-02 0.5143986 at 110iterations 1.4745870E-02 0.3251495 at 120iterations 8.2141822E-03 0.1641445 at 130iterations 4.5708679E-03 9.7518921E-02 at 140iterations 2.5440489E-03 4.9392700E-02 at 150iterations 1.4160027E-03 2.6777267E-02 at 160iterations 7.8866514E-04 1.6199112E-02 at 170iterations 4.3932648E-04 8.2807541E-03 at 180iterations finished qdiffx linear iterations at : 16:59:53 total time elapsed so far: 16.46000 # loops : 180 mean,max change (kT/e) : 4.3932648E-04 8.2807541E-03 energy calculations done at 16.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.64000 DelPhi exited at 16:59:54 16.643u 0.329s 0:17.33 97.8% 0+0k 0+0io 0pf+0w