Sat Oct 8 20:31:47 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 Sat Oct 8 2011 at 20:31:47 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2587 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 495 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: 0.6168347 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): -31.36300 17.45100 ymin,ymax (A): -23.17400 23.19900 zmin,zma (A): -12.52000 45.19400 x,y,z range (A): 48.81400 46.37300 57.71400 scale (grids/A): 0.6168347 object centre (A): -6.956000 1.2499809E-02 16.33700 number of atom coordinates read : 2587 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 393.4040 centred at (gu) : 88.50282 89.04450 89.67014 assigned negative charge : -389.4046 centred at (gu) : 88.41541 89.08603 89.53963 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6414 nv = 96 ne = 84 npr = 54259 no. pairs analyzed = 54259 no. exposed pairs = 3005 no. arc points = 21566 no. surface atoms = 1012 nbur = 1575 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 336 mr = 3584 m= 4 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 105 time to turn everything in is 0.3900000 number of dielectric boundary points 3135 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2124 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 7948 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4141549E-09 1.0042556E-08 midg,1,midg; midg,igrid,midg 6.8112760E-09 4.1731954E-10 1,midg,midg; igrid,midg,midg -3.3595744E-09 5.9449428E-09 gauss-seidel spectral radius is 0.9863842 estimated iterations to convergence 70 setup time was (sec) 0.7400000 now iterating at: 20:31:48 rms-change max change #iterations 0.1229336 18.41243 at 10iterations 1.1194993E-02 1.835812 at 20iterations 1.0237028E-03 0.1552219 at 30iterations 9.8918026E-05 1.4728546E-02 at 40iterations 1.0210871E-05 2.1152496E-03 at 50iterations finished qdiffx linear iterations at : 20:31:52 total time elapsed so far: 4.420000 # loops : 50 mean,max change (kT/e) : 1.0210871E-05 2.1152496E-03 energy calculations done at 4.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.630000 DelPhi exited at 20:31:52 4.634u 0.401s 0:05.32 94.5% 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 Sat Oct 8 2011 at 20:31:52 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2587 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 495 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: 1.850504 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): -31.36300 17.45100 ymin,ymax (A): -23.17400 23.19900 zmin,zma (A): -12.52000 45.19400 x,y,z range (A): 48.81400 46.37300 57.71400 scale (grids/A): 1.850504 object centre (A): -6.956000 1.2499809E-02 16.33700 number of atom coordinates read : 2587 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 393.4040 centred at (gu) : 85.50790 87.13303 89.00999 assigned negative charge : -389.4046 centred at (gu) : 85.24599 87.25796 88.61879 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 69937 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21566 grid for indexing accessible points = 1.400000 m= 23739 mr = 48942 m= 3214 mr = 17469 m= 127 mr = 1898 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 3930 time to turn everything in is 0.7000000 number of dielectric boundary points 28663 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 188 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 19222 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) : 0.6168347 object centre at (A) : -6.956000 1.2499809E-02 16.33700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9543817E-02 2.6780752E-02 midg,1,midg; midg,igrid,midg 1.1221667E-02 1.3803015E-03 1,midg,midg; igrid,midg,midg 5.2430644E-04 2.9848611E-02 gauss-seidel spectral radius is 0.9985495 estimated iterations to convergence 208 setup time was (sec) 1.030000 now iterating at: 20:31:54 rms-change max change #iterations 3.991268 161.5160 at 10iterations 1.822119 58.85495 at 20iterations 0.8316262 30.86821 at 30iterations 0.3803197 12.17549 at 40iterations 0.1746850 5.822052 at 50iterations 8.0216937E-02 2.955765 at 60iterations 3.6528070E-02 1.333782 at 70iterations 1.6745636E-02 0.5592155 at 80iterations 7.6588225E-03 0.2746708 at 90iterations 3.5008695E-03 0.1150627 at 100iterations 1.6097076E-03 5.8114052E-02 at 110iterations 7.3748862E-04 2.4179459E-02 at 120iterations finished qdiffx linear iterations at : 20:32:03 total time elapsed so far: 10.45000 # loops : 120 mean,max change (kT/e) : 7.3748862E-04 2.4179459E-02 energy calculations done at 10.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.67000 DelPhi exited at 20:32:04 10.672u 0.435s 0:11.39 97.4% 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 Sat Oct 8 2011 at 20:32:04 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2587 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 495 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: 2.775756 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): -31.36300 17.45100 ymin,ymax (A): -23.17400 23.19900 zmin,zma (A): -12.52000 45.19400 x,y,z range (A): 48.81400 46.37300 57.71400 scale (grids/A): 2.775756 object centre (A): -6.956000 1.2499809E-02 16.33700 number of atom coordinates read : 2587 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 393.4040 centred at (gu) : 83.26163 85.69952 88.51474 assigned negative charge : -389.4046 centred at (gu) : 82.86903 85.88685 87.92819 start vw surface at 0.1600000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 161803 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21566 grid for indexing accessible points = 1.400000 m= 78941 mr = 118419 m= 26153 mr = 64752 m= 5647 mr = 20890 m= 579 mr = 4119 m= 22 mr = 353 m= 0 mr = 6 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 13261 time to turn everything in is 1.800000 number of dielectric boundary points 64606 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 19631 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) : 1.850504 object centre at (A) : -6.956000 1.2499809E-02 16.33700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.2984418E-02 0.3604326 midg,1,midg; midg,igrid,midg 0.1348801 -8.7774387E-03 1,midg,midg; igrid,midg,midg -2.1077001E-03 0.4042949 gauss-seidel spectral radius is 0.9992294 estimated iterations to convergence 284 setup time was (sec) 2.170000 now iterating at: 20:32:06 rms-change max change #iterations 9.411936 372.2943 at 10iterations 5.401886 134.0650 at 20iterations 3.074255 63.15464 at 30iterations 1.754064 36.86574 at 40iterations 0.9961858 20.15937 at 50iterations 0.5671188 11.28104 at 60iterations 0.3221830 6.766093 at 70iterations 0.1826695 3.245478 at 80iterations 0.1039269 2.092972 at 90iterations 5.9075627E-02 1.128601 at 100iterations 3.3570752E-02 0.6753922 at 110iterations 1.9099671E-02 0.3736496 at 120iterations 1.0815464E-02 0.2005482 at 130iterations 6.1539630E-03 0.1127663 at 140iterations 3.4986117E-03 6.7237854E-02 at 150iterations 1.9946769E-03 3.5847187E-02 at 160iterations 1.1364162E-03 2.1179199E-02 at 170iterations 6.4942206E-04 1.3099670E-02 at 180iterations finished qdiffx linear iterations at : 20:32:22 total time elapsed so far: 17.66000 # loops : 180 mean,max change (kT/e) : 6.4942206E-04 1.3099670E-02 energy calculations done at 17.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.87000 DelPhi exited at 20:32:22 17.873u 0.435s 0:18.59 98.4% 0+0k 0+0io 0pf+0w