Tue Oct 11 00:17:45 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+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 Tue Oct 11 2011 at 00:17:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2552 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: 0.5577053 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): -19.81900 31.05200 ymin,ymax (A): 44.42100 108.2540 zmin,zma (A): 34.74300 79.35100 x,y,z range (A): 50.87100 63.83300 44.60800 scale (grids/A): 0.5577053 object centre (A): 5.616500 76.33749 57.04700 number of atom coordinates read : 2552 total number of charged atoms : 2413 net assigned charge : 8.000024 assigned positive charge : 384.1789 centred at (gu) : 88.87052 87.96325 89.65111 assigned negative charge : -376.1795 centred at (gu) : 88.88843 88.04403 89.48995 start vw surface at 0.2200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 5155 nv = 96 ne = 84 npr = 51181 no. pairs analyzed = 51181 no. exposed pairs = 3116 no. arc points = 21703 no. surface atoms = 1059 nbur = 1493 mkacc time = 0.1400000 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 = 1.540000 m= 195 mr = 2770 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.3900000 number of dielectric boundary points 2574 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2206 ## 300 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 6651 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.0826189E-10 1.9493887E-09 midg,1,midg; midg,igrid,midg 2.3843949E-09 5.0540683E-11 1,midg,midg; igrid,midg,midg 1.2024203E-09 4.7082543E-10 gauss-seidel spectral radius is 0.9833797 estimated iterations to convergence 64 setup time was (sec) 0.6900000 now iterating at: 00:17:46 rms-change max change #iterations 7.5650752E-02 14.03611 at 10iterations 6.3823150E-03 1.094635 at 20iterations 9.5557747E-04 0.2523766 at 30iterations 2.3870905E-04 6.3518524E-02 at 40iterations 6.1205850E-05 1.6468048E-02 at 50iterations finished qdiffx linear iterations at : 00:17:49 total time elapsed so far: 3.950000 # loops : 50 mean,max change (kT/e) : 6.1205850E-05 1.6468048E-02 energy calculations done at 3.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.180000 DelPhi exited at 00:17:50 4.188u 0.203s 0:04.97 88.1% 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 00:17:50 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2552 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: 1.673116 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): -19.81900 31.05200 ymin,ymax (A): 44.42100 108.2540 zmin,zma (A): 34.74300 79.35100 x,y,z range (A): 50.87100 63.83300 44.60800 scale (grids/A): 1.673116 object centre (A): 5.616500 76.33749 57.04700 number of atom coordinates read : 2552 total number of charged atoms : 2413 net assigned charge : 8.000024 assigned positive charge : 384.1789 centred at (gu) : 86.61105 83.88937 88.95285 assigned negative charge : -376.1795 centred at (gu) : 86.66496 84.13181 88.46957 start vw surface at 0.2000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 56929 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21703 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 17701 mr = 39157 m= 1897 mr = 12595 m= 50 mr = 1027 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 2841 time to turn everything in is 0.5700000 number of dielectric boundary points 23799 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 246 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 18614 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) : 0.5577053 object centre at (A) : 5.616500 76.33749 57.04700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4808249E-03 1.3805859E-02 midg,1,midg; midg,igrid,midg -1.3993114E-02 7.3428177E-03 1,midg,midg; igrid,midg,midg 4.6489108E-03 6.1247759E-03 gauss-seidel spectral radius is 0.9982228 estimated iterations to convergence 188 setup time was (sec) 0.9300000 now iterating at: 00:17:51 rms-change max change #iterations 3.182123 157.8770 at 10iterations 1.326685 56.93394 at 20iterations 0.5587198 22.70467 at 30iterations 0.2357939 8.412981 at 40iterations 9.9460550E-02 4.211489 at 50iterations 4.2226825E-02 1.681002 at 60iterations 1.7977858E-02 0.6701050 at 70iterations 7.7891978E-03 0.3158073 at 80iterations 3.4607351E-03 0.1567459 at 90iterations 1.6446665E-03 7.6202393E-02 at 100iterations 8.4940612E-04 4.2282104E-02 at 110iterations 4.7144108E-04 2.5749207E-02 at 120iterations finished qdiffx linear iterations at : 00:17:59 total time elapsed so far: 9.270000 # loops : 120 mean,max change (kT/e) : 4.7144108E-04 2.5749207E-02 energy calculations done at 9.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.500000 DelPhi exited at 00:18:00 9.501u 0.234s 0:10.11 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 Tue Oct 11 2011 at 00:18:00 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2552 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: 2.509674 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): -19.81900 31.05200 ymin,ymax (A): 44.42100 108.2540 zmin,zma (A): 34.74300 79.35100 x,y,z range (A): 50.87100 63.83300 44.60800 scale (grids/A): 2.509674 object centre (A): 5.616500 76.33749 57.04700 number of atom coordinates read : 2552 total number of charged atoms : 2413 net assigned charge : 8.000024 assigned positive charge : 384.1789 centred at (gu) : 84.91651 80.83388 88.42919 assigned negative charge : -376.1795 centred at (gu) : 84.99736 81.19760 87.70423 start vw surface at 0.2000000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 132096 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21703 grid for indexing accessible points = 1.400000 m= 61160 mr = 95325 m= 17922 mr = 49162 m= 3111 mr = 13976 m= 175 mr = 2125 m= 1 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 9696 time to turn everything in is 1.300000 number of dielectric boundary points 53808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 19289 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) : 1.673116 object centre at (A) : 5.616500 76.33749 57.04700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8161820E-02 0.1598723 midg,1,midg; midg,igrid,midg -0.4517849 7.6007724E-02 1,midg,midg; igrid,midg,midg 2.3453517E-02 6.8094686E-02 gauss-seidel spectral radius is 0.9991315 estimated iterations to convergence 268 setup time was (sec) 1.680000 now iterating at: 00:18:02 rms-change max change #iterations 7.990947 310.2659 at 10iterations 4.398807 100.1435 at 20iterations 2.422042 62.36185 at 30iterations 1.331843 28.78530 at 40iterations 0.7281991 16.46782 at 50iterations 0.4001501 8.671312 at 60iterations 0.2188505 4.588292 at 70iterations 0.1204083 2.550903 at 80iterations 6.5969698E-02 1.383213 at 90iterations 3.6045250E-02 0.7417984 at 100iterations 1.9849807E-02 0.4753532 at 110iterations 1.0975144E-02 0.2508965 at 120iterations 6.1010793E-03 0.1303444 at 130iterations 3.4372492E-03 8.6997986E-02 at 140iterations 1.9909861E-03 5.7811737E-02 at 150iterations 1.1993377E-03 3.6624908E-02 at 160iterations 7.5709214E-04 2.1369934E-02 at 170iterations 5.0307967E-04 1.4881134E-02 at 180iterations finished qdiffx linear iterations at : 00:18:16 total time elapsed so far: 15.74000 # loops : 180 mean,max change (kT/e) : 5.0307967E-04 1.4881134E-02 energy calculations done at 15.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.98000 DelPhi exited at 00:18:17 15.980u 0.237s 0:16.70 97.0% 0+0k 0+0io 0pf+0w