Wed Apr 18 19:28:06 PDT 2012 #!/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 Wed Apr 18 2012 at 19:28:06 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 ! Automatically converted by prot2crg.py # of charge parameter records: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3035 !!! WARNING: TPO 165 has a net charge of -1.7500 !!! WARNING: GLU 329 has a net charge of -2.0000 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: 0.5767330 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): -23.95000 27.49100 ymin,ymax (A): -26.24800 24.80700 zmin,zma (A): -8.739000 52.98800 x,y,z range (A): 51.44100 51.05500 61.72701 scale (grids/A): 0.5767330 object centre (A): 1.770501 -0.7205009 22.12450 number of atom coordinates read : 3035 total number of charged atoms : 2914 net assigned charge : 2.250037 assigned positive charge : 460.5828 centred at (gu) : 91.09735 89.95100 90.14492 assigned negative charge : -458.3339 centred at (gu) : 91.21964 89.93498 90.25753 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6648 nv = 96 ne = 84 npr = 60918 no. pairs analyzed = 60918 no. exposed pairs = 3950 no. arc points = 27702 no. surface atoms = 1321 nbur = 1714 mkacc time = 0.1200000 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= 314 mr = 3516 m= 4 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3431 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2822 ## 342 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 8617 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6424773E-09 -1.9114179E-09 midg,1,midg; midg,igrid,midg 1.5099198E-10 7.9162643E-10 1,midg,midg; igrid,midg,midg 2.2581359E-09 -2.6766223E-09 gauss-seidel spectral radius is 0.9844902 estimated iterations to convergence 66 setup time was (sec) 0.4400000 now iterating at: 19:28:07 rms-change max change #iterations 9.7384974E-02 16.55558 at 10iterations 7.7517284E-03 1.054260 at 20iterations 1.0135754E-03 0.1880016 at 30iterations 3.5913350E-04 8.0190659E-02 at 40iterations 1.5458582E-04 3.4961700E-02 at 50iterations finished qdiffx linear iterations at : 19:28:10 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 1.5458582E-04 3.4961700E-02 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 19:28:10 3.557u 0.195s 0:04.04 92.5% 0+0k 0+45992io 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 Apr 18 2012 at 19:28:10 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 ! Automatically converted by prot2crg.py # of charge parameter records: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3035 !!! WARNING: TPO 165 has a net charge of -1.7500 !!! WARNING: GLU 329 has a net charge of -2.0000 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: 1.730199 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): -23.95000 27.49100 ymin,ymax (A): -26.24800 24.80700 zmin,zma (A): -8.739000 52.98800 x,y,z range (A): 51.44100 51.05500 61.72701 scale (grids/A): 1.730199 object centre (A): 1.770501 -0.7205009 22.12450 number of atom coordinates read : 3035 total number of charged atoms : 2914 net assigned charge : 2.250037 assigned positive charge : 460.5828 centred at (gu) : 93.29128 89.85182 90.43392 assigned negative charge : -458.3339 centred at (gu) : 93.65845 89.80462 90.77225 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 73497 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27702 grid for indexing accessible points = 1.400000 m= 23468 mr = 50126 m= 2708 mr = 16289 m= 87 mr = 1407 m= 0 mr = 7 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 181 time to turn everything in is 0.4400000 number of dielectric boundary points 31931 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 271 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 22596 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) : 0.5767330 object centre at (A) : 1.770501 -0.7205009 22.12450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3468035E-02 2.0361828E-02 midg,1,midg; midg,igrid,midg 1.0317702E-04 1.3682684E-03 1,midg,midg; igrid,midg,midg 4.5179417E-03 -9.7584780E-03 gauss-seidel spectral radius is 0.9984033 estimated iterations to convergence 199 setup time was (sec) 0.6600000 now iterating at: 19:28:11 rms-change max change #iterations 3.844236 188.6273 at 10iterations 1.684045 54.47189 at 20iterations 0.7412867 26.59837 at 30iterations 0.3263602 11.40757 at 40iterations 0.1441165 5.028387 at 50iterations 6.3196033E-02 2.062326 at 60iterations 2.7997721E-02 0.8693981 at 70iterations 1.2466284E-02 0.4215508 at 80iterations 5.6820763E-03 0.2299252 at 90iterations 2.7380765E-03 0.1014977 at 100iterations 1.4548646E-03 6.0970306E-02 at 110iterations 8.9400285E-04 3.9867401E-02 at 120iterations finished qdiffx linear iterations at : 19:28:19 total time elapsed so far: 7.910000 # loops : 120 mean,max change (kT/e) : 8.9400285E-04 3.9867401E-02 energy calculations done at 7.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.050000 DelPhi exited at 19:28:19 8.056u 0.203s 0:08.54 96.6% 0+0k 0+45320io 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 Apr 18 2012 at 19:28:19 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 ! Automatically converted by prot2crg.py # of charge parameter records: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3035 !!! WARNING: TPO 165 has a net charge of -1.7500 !!! WARNING: GLU 329 has a net charge of -2.0000 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: 2.595299 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): -23.95000 27.49100 ymin,ymax (A): -26.24800 24.80700 zmin,zma (A): -8.739000 52.98800 x,y,z range (A): 51.44100 51.05500 61.72701 scale (grids/A): 2.595299 object centre (A): 1.770501 -0.7205009 22.12450 number of atom coordinates read : 3035 total number of charged atoms : 2914 net assigned charge : 2.250037 assigned positive charge : 460.5828 centred at (gu) : 94.93670 89.77743 90.65054 assigned negative charge : -458.3339 centred at (gu) : 95.48769 89.70683 91.15843 start vw surface at 0.1000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 170409 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27702 grid for indexing accessible points = 1.400000 m= 80553 mr = 122266 m= 24184 mr = 64180 m= 4491 mr = 18307 m= 384 mr = 2983 m= 5 mr = 178 m= 0 mr = 3 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 619 time to turn everything in is 1.140000 number of dielectric boundary points 72109 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 23298 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) : 1.730199 object centre at (A) : 1.770501 -0.7205009 22.12450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6817840E-02 0.5398222 midg,1,midg; midg,igrid,midg 6.7849760E-04 1.9663610E-02 1,midg,midg; igrid,midg,midg 2.3770068E-02 -0.1125776 gauss-seidel spectral radius is 0.9992101 estimated iterations to convergence 281 setup time was (sec) 1.360000 now iterating at: 19:28:21 rms-change max change #iterations 9.587020 323.4659 at 10iterations 5.518007 130.7676 at 20iterations 3.181853 68.55083 at 30iterations 1.815953 39.93716 at 40iterations 1.036513 22.13147 at 50iterations 0.5884753 12.71407 at 60iterations 0.3348007 6.996724 at 70iterations 0.1899295 4.036510 at 80iterations 0.1078315 2.130663 at 90iterations 6.0978997E-02 1.150330 at 100iterations 3.4583647E-02 0.6892385 at 110iterations 1.9582251E-02 0.4042772 at 120iterations 1.1159074E-02 0.2241440 at 130iterations 6.4218612E-03 0.1286373 at 140iterations 3.7616724E-03 8.4903717E-02 at 150iterations 2.2867846E-03 5.4935455E-02 at 160iterations 1.4741668E-03 3.5593033E-02 at 170iterations 1.0224779E-03 2.6117325E-02 at 180iterations finished qdiffx linear iterations at : 19:28:32 total time elapsed so far: 12.81000 # loops : 180 mean,max change (kT/e) : 1.0224779E-03 2.6117325E-02 energy calculations done at 12.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.95000 DelPhi exited at 19:28:32 12.950u 0.233s 0:13.47 97.8% 0+0k 0+45312io 0pf+0w