Sun Oct 9 02:52:02 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 Sun Oct 9 2011 at 02:52:02 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2511 !!! WARNING: SEP 117 has a net charge of -0.4750 !!! WARNING: GLM 118 has a net charge of -0.0940 !!! WARNING: HIT 140 has a net charge of 0.5140 !!! WARNING: MG4 428 has a net charge of 1.4000 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: 0.6227042 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): -40.86800 16.30200 ymin,ymax (A): -21.07100 27.49200 zmin,zma (A): -53.23300 -0.1090001 x,y,z range (A): 57.17000 48.56300 53.12400 scale (grids/A): 0.6227042 object centre (A): -12.28300 3.210500 -26.67100 number of atom coordinates read : 2511 total number of charged atoms : 2371 net assigned charge : -2.154983 assigned positive charge : 383.7491 centred at (gu) : 88.66030 90.13038 90.80718 assigned negative charge : -385.9048 centred at (gu) : 88.62269 90.17249 90.80271 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6429 nv = 96 ne = 84 npr = 50719 no. pairs analyzed = 50719 no. exposed pairs = 3101 no. arc points = 21819 no. surface atoms = 1029 nbur = 1482 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 299 mr = 3503 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 198 time to turn everything in is 0.3100000 number of dielectric boundary points 3202 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2167 ## 227 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7904 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8160252E-09 -1.7985493E-09 midg,1,midg; midg,igrid,midg 1.1152952E-09 -4.9937290E-09 1,midg,midg; igrid,midg,midg -6.0879572E-09 5.9754229E-10 gauss-seidel spectral radius is 0.9866369 estimated iterations to convergence 71 setup time was (sec) 0.5300000 now iterating at: 02:52:03 rms-change max change #iterations 0.1295428 19.19569 at 10iterations 1.2039924E-02 1.871429 at 20iterations 1.1207431E-03 0.1643600 at 30iterations 1.0469809E-04 1.6005993E-02 at 40iterations 9.7279808E-06 1.3198853E-03 at 50iterations finished qdiffx linear iterations at : 02:52:05 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 9.7279808E-06 1.3198853E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 02:52:05 3.139u 0.125s 0:03.58 90.7% 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 Sun Oct 9 2011 at 02:52:06 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 # of charge parameter records: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2511 !!! WARNING: SEP 117 has a net charge of -0.4750 !!! WARNING: GLM 118 has a net charge of -0.0940 !!! WARNING: HIT 140 has a net charge of 0.5140 !!! WARNING: MG4 428 has a net charge of 1.4000 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: 1.868113 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): -40.86800 16.30200 ymin,ymax (A): -21.07100 27.49200 zmin,zma (A): -53.23300 -0.1090001 x,y,z range (A): 57.17000 48.56300 53.12400 scale (grids/A): 1.868113 object centre (A): -12.28300 3.210500 -26.67100 number of atom coordinates read : 2511 total number of charged atoms : 2371 net assigned charge : -2.154983 assigned positive charge : 383.7491 centred at (gu) : 85.98045 90.39085 92.42092 assigned negative charge : -385.9048 centred at (gu) : 85.86791 90.51709 92.40801 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 70315 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21819 grid for indexing accessible points = 1.400000 m= 23961 mr = 48419 m= 3348 mr = 17498 m= 144 mr = 2041 m= 2 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 6308 time to turn everything in is 0.4900000 number of dielectric boundary points 29768 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 127 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 18579 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) : 0.6227042 object centre at (A) : -12.28300 3.210500 -26.67100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2965531E-04 1.3570793E-03 midg,1,midg; midg,igrid,midg 3.5078134E-03 -1.5648905E-02 1,midg,midg; igrid,midg,midg -7.1914867E-03 2.5293069E-02 gauss-seidel spectral radius is 0.9985768 estimated iterations to convergence 210 setup time was (sec) 0.7600000 now iterating at: 02:52:06 rms-change max change #iterations 4.112764 173.3404 at 10iterations 1.888570 67.93275 at 20iterations 0.8694436 28.80486 at 30iterations 0.4014182 12.49179 at 40iterations 0.1847465 6.396355 at 50iterations 8.5107677E-02 2.778870 at 60iterations 3.9160933E-02 1.352028 at 70iterations 1.8005479E-02 0.5980563 at 80iterations 8.3323885E-03 0.2766953 at 90iterations 3.8421070E-03 0.1228662 at 100iterations 1.7699990E-03 5.6922913E-02 at 110iterations 8.1615034E-04 2.7287483E-02 at 120iterations finished qdiffx linear iterations at : 02:52:13 total time elapsed so far: 6.830000 # loops : 120 mean,max change (kT/e) : 8.1615034E-04 2.7287483E-02 energy calculations done at 6.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.990000 DelPhi exited at 02:52:13 6.994u 0.160s 0:07.43 96.2% 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 Sun Oct 9 2011 at 02:52:13 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2511 !!! WARNING: SEP 117 has a net charge of -0.4750 !!! WARNING: GLM 118 has a net charge of -0.0940 !!! WARNING: HIT 140 has a net charge of 0.5140 !!! WARNING: MG4 428 has a net charge of 1.4000 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: 2.802169 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): -40.86800 16.30200 ymin,ymax (A): -21.07100 27.49200 zmin,zma (A): -53.23300 -0.1090001 x,y,z range (A): 57.17000 48.56300 53.12400 scale (grids/A): 2.802169 object centre (A): -12.28300 3.210500 -26.67100 number of atom coordinates read : 2511 total number of charged atoms : 2371 net assigned charge : -2.154983 assigned positive charge : 383.7491 centred at (gu) : 83.97055 90.58615 93.63122 assigned negative charge : -385.9048 centred at (gu) : 83.80183 90.77563 93.61194 start vw surface at 0.1300000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 162827 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21819 grid for indexing accessible points = 1.400000 m= 79104 mr = 117726 m= 26734 mr = 64240 m= 5782 mr = 21371 m= 692 mr = 4308 m= 21 mr = 464 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 21261 time to turn everything in is 1.150000 number of dielectric boundary points 67042 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 18967 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) : 1.868113 object centre at (A) : -12.28300 3.210500 -26.67100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0493297E-02 0.1034621 midg,1,midg; midg,igrid,midg 5.8065999E-02 -0.2270001 1,midg,midg; igrid,midg,midg -0.1662327 0.3348147 gauss-seidel spectral radius is 0.9992436 estimated iterations to convergence 287 setup time was (sec) 1.430000 now iterating at: 02:52:15 rms-change max change #iterations 9.776400 297.3134 at 10iterations 5.718137 153.0063 at 20iterations 3.314116 90.74779 at 30iterations 1.919849 44.18506 at 40iterations 1.105020 25.89130 at 50iterations 0.6360329 13.34581 at 60iterations 0.3661149 7.870758 at 70iterations 0.2098387 4.501496 at 80iterations 0.1200059 2.534580 at 90iterations 6.8808176E-02 1.415762 at 100iterations 3.9380603E-02 0.7470398 at 110iterations 2.2538321E-02 0.4647585 at 120iterations 1.2884326E-02 0.2744141 at 130iterations 7.3778629E-03 0.1442394 at 140iterations 4.2105955E-03 8.3468437E-02 at 150iterations 2.4047650E-03 5.0336838E-02 at 160iterations 1.3737703E-03 3.1106949E-02 at 170iterations 7.8507740E-04 1.5411377E-02 at 180iterations finished qdiffx linear iterations at : 02:52:24 total time elapsed so far: 10.87000 # loops : 180 mean,max change (kT/e) : 7.8507740E-04 1.5411377E-02 energy calculations done at 10.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.04000 DelPhi exited at 02:52:25 11.043u 0.186s 0:11.50 97.5% 0+0k 0+0io 0pf+0w