Sat Oct 8 11:38:03 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 11:38:03 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3364 !!! WARNING: HIR 14 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6360664 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): 32.21600 81.65600 ymin,ymax (A): 25.58900 81.55800 zmin,zma (A): -3.330000 46.68000 x,y,z range (A): 49.43999 55.96900 50.01000 scale (grids/A): 0.6360664 object centre (A): 56.93600 53.57350 21.67500 number of atom coordinates read : 3364 total number of charged atoms : 3213 net assigned charge : -4.485962 assigned positive charge : 513.6103 centred at (gu) : 90.90283 89.43072 91.09267 assigned negative charge : -518.0974 centred at (gu) : 90.69562 89.51479 91.10577 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8877 nv = 96 ne = 84 npr = 71543 no. pairs analyzed = 71543 no. exposed pairs = 3792 no. arc points = 25378 no. surface atoms = 1310 nbur = 2054 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 517 mr = 5356 m= 1 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.3900000 number of dielectric boundary points 3975 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2467 ## 220 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 10878 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.4469834E-09 -1.0030677E-08 midg,1,midg; midg,igrid,midg 6.2821930E-09 -1.5898419E-08 1,midg,midg; igrid,midg,midg -2.9370931E-08 2.7103743E-08 gauss-seidel spectral radius is 0.9872493 estimated iterations to convergence 72 setup time was (sec) 0.6300000 now iterating at: 11:38:04 rms-change max change #iterations 0.1694339 23.83484 at 10iterations 1.6596418E-02 2.170666 at 20iterations 1.7050201E-03 0.2104759 at 30iterations 1.8084017E-04 2.4044991E-02 at 40iterations 2.4155668E-05 3.2124519E-03 at 50iterations finished qdiffx linear iterations at : 11:38:06 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 2.4155668E-05 3.2124519E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 11:38:07 3.502u 0.159s 0:04.07 89.6% 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 11:38:07 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3364 !!! WARNING: HIR 14 has a net charge of 0.5140 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: 1.908199 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): 32.21600 81.65600 ymin,ymax (A): 25.58900 81.55800 zmin,zma (A): -3.330000 46.68000 x,y,z range (A): 49.43999 55.96900 50.01000 scale (grids/A): 1.908199 object centre (A): 56.93600 53.57350 21.67500 number of atom coordinates read : 3364 total number of charged atoms : 3213 net assigned charge : -4.485962 assigned positive charge : 513.6103 centred at (gu) : 92.70742 88.29158 93.27688 assigned negative charge : -518.0974 centred at (gu) : 92.08640 88.54391 93.31670 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 96773 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25378 grid for indexing accessible points = 1.400000 m= 36543 mr = 70815 m= 5913 mr = 28138 m= 356 mr = 3962 m= 5 mr = 126 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 444 time to turn everything in is 0.7100000 number of dielectric boundary points 36549 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 132 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 25248 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) : 0.6360664 object centre at (A) : 56.93600 53.57350 21.67500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9848082E-02 -4.9443189E-02 midg,1,midg; midg,igrid,midg 2.0690512E-02 -3.8306270E-02 1,midg,midg; igrid,midg,midg -3.6049411E-02 3.3061810E-02 gauss-seidel spectral radius is 0.9986976 estimated iterations to convergence 220 setup time was (sec) 1.010000 now iterating at: 11:38:08 rms-change max change #iterations 5.035550 213.9736 at 10iterations 2.395629 68.29137 at 20iterations 1.141768 37.34222 at 30iterations 0.5475532 15.21492 at 40iterations 0.2608456 6.810139 at 50iterations 0.1248145 3.352081 at 60iterations 5.9414137E-02 1.841145 at 70iterations 2.8434336E-02 0.7732496 at 80iterations 1.3568711E-02 0.3738037 at 90iterations 6.4918138E-03 0.1784897 at 100iterations 3.1069855E-03 8.3308935E-02 at 110iterations 1.4889276E-03 4.4672012E-02 at 120iterations finished qdiffx linear iterations at : 11:38:15 total time elapsed so far: 7.960000 # loops : 120 mean,max change (kT/e) : 1.4889276E-03 4.4672012E-02 energy calculations done at 7.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.150000 DelPhi exited at 11:38:16 8.149u 0.223s 0:08.74 95.6% 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 11:38:16 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3364 !!! WARNING: HIR 14 has a net charge of 0.5140 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: 2.862299 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): 32.21600 81.65600 ymin,ymax (A): 25.58900 81.55800 zmin,zma (A): -3.330000 46.68000 x,y,z range (A): 49.43999 55.96900 50.01000 scale (grids/A): 2.862299 object centre (A): 56.93600 53.57350 21.67500 number of atom coordinates read : 3364 total number of charged atoms : 3213 net assigned charge : -4.485962 assigned positive charge : 513.6103 centred at (gu) : 94.06068 87.43712 94.91533 assigned negative charge : -518.0974 centred at (gu) : 93.12951 87.81567 94.97478 start vw surface at 0.1700000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 223983 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25378 grid for indexing accessible points = 1.400000 m= 117586 mr = 170485 m= 44141 mr = 98902 m= 10811 mr = 36855 m= 1572 mr = 8370 m= 85 mr = 1081 m= 1 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 1460 time to turn everything in is 1.850000 number of dielectric boundary points 82447 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 25700 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) : 1.908199 object centre at (A) : 56.93600 53.57350 21.67500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2580893 -0.4921370 midg,1,midg; midg,igrid,midg 0.3350398 -0.2824720 1,midg,midg; igrid,midg,midg -0.3432579 0.3958416 gauss-seidel spectral radius is 0.9992798 estimated iterations to convergence 294 setup time was (sec) 2.190000 now iterating at: 11:38:18 rms-change max change #iterations 11.59381 315.3602 at 10iterations 6.835595 138.5233 at 20iterations 3.994833 75.01022 at 30iterations 2.333429 40.45071 at 40iterations 1.360256 24.22408 at 50iterations 0.7909753 13.08389 at 60iterations 0.4600573 7.803679 at 70iterations 0.2667943 4.580889 at 80iterations 0.1549723 2.327179 at 90iterations 8.9908205E-02 1.501668 at 100iterations 5.2152272E-02 0.8570290 at 110iterations 3.0223122E-02 0.4689388 at 120iterations 1.7507624E-02 0.2640505 at 130iterations 1.0158454E-02 0.1684799 at 140iterations 5.8954027E-03 8.8659286E-02 at 150iterations 3.4226424E-03 6.1017990E-02 at 160iterations 1.9870331E-03 3.2234192E-02 at 170iterations 1.1619970E-03 1.8640041E-02 at 180iterations finished qdiffx linear iterations at : 11:38:29 total time elapsed so far: 13.35000 # loops : 180 mean,max change (kT/e) : 1.1619970E-03 1.8640041E-02 energy calculations done at 13.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.54000 DelPhi exited at 11:38:30 13.537u 0.227s 0:14.48 94.9% 0+0k 0+0io 0pf+0w