Tue Oct 11 06:41:30 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 Tue Oct 11 2011 at 06:41:30 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2011 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7345507 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): -20.00800 23.83900 ymin,ymax (A): -11.21700 28.31000 zmin,zma (A): -3.318000 45.14700 x,y,z range (A): 43.84700 39.52700 48.46500 scale (grids/A): 0.7345507 object centre (A): 1.915501 8.546499 20.91450 number of atom coordinates read : 2011 total number of charged atoms : 1914 net assigned charge : 6.025006 assigned positive charge : 309.6751 centred at (gu) : 90.02312 89.42286 91.17179 assigned negative charge : -303.6502 centred at (gu) : 89.84277 89.45329 91.25030 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7448 nv = 96 ne = 84 npr = 40192 no. pairs analyzed = 40192 no. exposed pairs = 2428 no. arc points = 16526 no. surface atoms = 826 nbur = 1185 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 566 mr = 4404 m= 6 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3500 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1522 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 8169 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3049345E-07 3.2203424E-08 midg,1,midg; midg,igrid,midg 1.3476797E-07 6.2116037E-08 1,midg,midg; igrid,midg,midg -6.2583304E-08 2.4863294E-07 gauss-seidel spectral radius is 0.9903259 estimated iterations to convergence 83 setup time was (sec) 0.3500000 now iterating at: 06:41:31 rms-change max change #iterations 0.2364124 28.41291 at 10iterations 3.2108124E-02 4.616942 at 20iterations 4.3916106E-03 0.5966606 at 30iterations 6.7979418E-04 8.8855743E-02 at 40iterations 1.4663137E-04 1.8136978E-02 at 50iterations finished qdiffx linear iterations at : 06:41:34 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 1.4663137E-04 1.8136978E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 06:41:34 3.291u 0.172s 0:03.84 90.1% 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 06:41:34 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2011 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.203652 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): -20.00800 23.83900 ymin,ymax (A): -11.21700 28.31000 zmin,zma (A): -3.318000 45.14700 x,y,z range (A): 43.84700 39.52700 48.46500 scale (grids/A): 2.203652 object centre (A): 1.915501 8.546499 20.91450 number of atom coordinates read : 2011 total number of charged atoms : 1914 net assigned charge : 6.025006 assigned positive charge : 309.6751 centred at (gu) : 90.06924 88.26873 93.51547 assigned negative charge : -303.6502 centred at (gu) : 89.52824 88.35983 93.75079 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 78804 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16526 grid for indexing accessible points = 1.400000 m= 32615 mr = 56636 m= 6936 mr = 25086 m= 709 mr = 4809 m= 19 mr = 392 m= 0 mr = 3 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 32157 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 57 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 15235 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) : 0.7345507 object centre at (A) : 1.915501 8.546499 20.91450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4749737E-02 3.5874363E-02 midg,1,midg; midg,igrid,midg 4.0849965E-02 5.8833342E-03 1,midg,midg; igrid,midg,midg 1.8285038E-02 5.3719833E-02 gauss-seidel spectral radius is 0.9988961 estimated iterations to convergence 238 setup time was (sec) 0.6100000 now iterating at: 06:41:35 rms-change max change #iterations 4.914585 242.0918 at 10iterations 2.473795 84.58287 at 20iterations 1.259540 38.28761 at 30iterations 0.6400125 18.20750 at 40iterations 0.3222668 10.32876 at 50iterations 0.1639679 5.326029 at 60iterations 8.3027318E-02 2.319722 at 70iterations 4.2167354E-02 1.272523 at 80iterations 2.1371303E-02 0.7337599 at 90iterations 1.0895825E-02 0.3157272 at 100iterations 5.5691982E-03 0.1573792 at 110iterations 2.8520920E-03 8.2378387E-02 at 120iterations finished qdiffx linear iterations at : 06:41:42 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 2.8520920E-03 8.2378387E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 06:41:42 7.700u 0.183s 0:08.37 94.1% 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 06:41:43 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2011 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.305478 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): -20.00800 23.83900 ymin,ymax (A): -11.21700 28.31000 zmin,zma (A): -3.318000 45.14700 x,y,z range (A): 43.84700 39.52700 48.46500 scale (grids/A): 3.305478 object centre (A): 1.915501 8.546499 20.91450 number of atom coordinates read : 2011 total number of charged atoms : 1914 net assigned charge : 6.025006 assigned positive charge : 309.6751 centred at (gu) : 90.10386 87.40309 95.27322 assigned negative charge : -303.6502 centred at (gu) : 89.29240 87.53982 95.62624 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 181552 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16526 grid for indexing accessible points = 1.400000 m= 100629 mr = 135837 m= 42435 mr = 84586 m= 13180 mr = 35319 m= 2893 mr = 10474 m= 398 mr = 2241 m= 19 mr = 292 m= 0 mr = 7 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 72350 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 15312 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) : 2.203652 object centre at (A) : 1.915501 8.546499 20.91450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2708108 0.3479662 midg,1,midg; midg,igrid,midg 0.3056026 2.2888562E-02 1,midg,midg; igrid,midg,midg 0.3353358 0.3990186 gauss-seidel spectral radius is 0.9993094 estimated iterations to convergence 300 setup time was (sec) 1.450000 now iterating at: 06:41:44 rms-change max change #iterations 10.62906 318.2612 at 10iterations 6.330015 145.1432 at 20iterations 3.755810 81.89523 at 30iterations 2.237174 46.74128 at 40iterations 1.321462 25.73906 at 50iterations 0.7807630 14.23743 at 60iterations 0.4606068 7.997250 at 70iterations 0.2712279 4.366694 at 80iterations 0.1604982 3.046028 at 90iterations 9.4628021E-02 1.590130 at 100iterations 5.5837236E-02 0.9538765 at 110iterations 3.3095852E-02 0.5543332 at 120iterations 1.9744888E-02 0.3642635 at 130iterations 1.1878665E-02 0.1958532 at 140iterations 7.3395213E-03 0.1382256 at 150iterations 4.6926658E-03 9.8396301E-02 at 160iterations 3.1351731E-03 6.0691833E-02 at 170iterations 2.2273895E-03 3.9146423E-02 at 180iterations finished qdiffx linear iterations at : 06:41:55 total time elapsed so far: 12.58000 # loops : 180 mean,max change (kT/e) : 2.2273895E-03 3.9146423E-02 energy calculations done at 12.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.72000 DelPhi exited at 06:41:56 12.720u 0.196s 0:13.47 95.8% 0+0k 0+0io 0pf+0w