Mon Oct 10 10:36:50 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 Mon Oct 10 2011 at 10:36:50 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2942 !!! WARNING: HIT 235 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5718783 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): -21.17300 41.07800 ymin,ymax (A): -12.02800 46.08700 zmin,zma (A): -1.903000 51.97400 x,y,z range (A): 62.25100 58.11500 53.87700 scale (grids/A): 0.5718783 object centre (A): 9.952501 17.02950 25.03550 number of atom coordinates read : 2942 total number of charged atoms : 2788 net assigned charge : 5.014020 assigned positive charge : 432.2467 centred at (gu) : 92.25751 91.35665 86.44873 assigned negative charge : -427.2332 centred at (gu) : 92.30742 91.45078 86.25452 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6430 nv = 96 ne = 84 npr = 57384 no. pairs analyzed = 57384 no. exposed pairs = 4505 no. arc points = 32075 no. surface atoms = 1492 nbur = 1450 mkacc time = 0.1500000 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 = 1.512000 m= 295 mr = 2811 m= 4 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3901 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3158 ## 351 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8173 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2347686E-09 1.7194759E-09 midg,1,midg; midg,igrid,midg 1.7646115E-09 -7.4127793E-10 1,midg,midg; igrid,midg,midg 1.0337461E-09 2.8329308E-10 gauss-seidel spectral radius is 0.9842353 estimated iterations to convergence 65 setup time was (sec) 0.6300000 now iterating at: 10:36:51 rms-change max change #iterations 9.4951302E-02 18.85757 at 10iterations 7.0048743E-03 1.222369 at 20iterations 5.2271842E-04 8.4770203E-02 at 30iterations 4.7750465E-05 7.0514679E-03 at 40iterations 7.2801186E-06 1.0089874E-03 at 50iterations finished qdiffx linear iterations at : 10:36:55 total time elapsed so far: 4.820000 # loops : 50 mean,max change (kT/e) : 7.2801186E-06 1.0089874E-03 energy calculations done at 4.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.000000 DelPhi exited at 10:36:56 5.001u 0.459s 0:05.75 94.7% 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 Mon Oct 10 2011 at 10:36:56 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2942 !!! WARNING: HIT 235 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.715635 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): -21.17300 41.07800 ymin,ymax (A): -12.02800 46.08700 zmin,zma (A): -1.903000 51.97400 x,y,z range (A): 62.25100 58.11500 53.87700 scale (grids/A): 1.715635 object centre (A): 9.952501 17.02950 25.03550 number of atom coordinates read : 2942 total number of charged atoms : 2788 net assigned charge : 5.014020 assigned positive charge : 432.2467 centred at (gu) : 96.77193 94.06960 79.34565 assigned negative charge : -427.2332 centred at (gu) : 96.92177 94.35196 78.76333 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 69378 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32075 grid for indexing accessible points = 1.400000 m= 21584 mr = 42382 m= 2591 mr = 13813 m= 87 mr = 1168 m= 2 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 36269 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 294 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 21559 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) : 0.5718783 object centre at (A) : 9.952501 17.02950 25.03550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6363787E-02 1.0393712E-02 midg,1,midg; midg,igrid,midg 2.2612063E-02 6.0037132E-03 1,midg,midg; igrid,midg,midg -1.4487213E-02 -1.0002728E-02 gauss-seidel spectral radius is 0.9983651 estimated iterations to convergence 196 setup time was (sec) 0.9400000 now iterating at: 10:36:57 rms-change max change #iterations 3.621720 164.3020 at 10iterations 1.564830 58.12961 at 20iterations 0.6765063 25.99786 at 30iterations 0.2930808 10.31735 at 40iterations 0.1277348 4.341384 at 50iterations 5.5377264E-02 1.983568 at 60iterations 2.4162721E-02 0.8456726 at 70iterations 1.0512250E-02 0.4249077 at 80iterations 4.5615137E-03 0.1572466 at 90iterations 1.9811566E-03 7.0708752E-02 at 100iterations 8.5925916E-04 2.6969910E-02 at 110iterations 3.7591904E-04 1.3732910E-02 at 120iterations finished qdiffx linear iterations at : 10:37:08 total time elapsed so far: 11.87000 # loops : 120 mean,max change (kT/e) : 3.7591904E-04 1.3732910E-02 energy calculations done at 11.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.03000 DelPhi exited at 10:37:09 12.037u 0.499s 0:12.79 97.8% 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 Mon Oct 10 2011 at 10:37:09 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2942 !!! WARNING: HIT 235 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.573452 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): -21.17300 41.07800 ymin,ymax (A): -12.02800 46.08700 zmin,zma (A): -1.903000 51.97400 x,y,z range (A): 62.25100 58.11500 53.87700 scale (grids/A): 2.573452 object centre (A): 9.952501 17.02950 25.03550 number of atom coordinates read : 2942 total number of charged atoms : 2788 net assigned charge : 5.014020 assigned positive charge : 432.2467 centred at (gu) : 100.1578 96.10432 74.01842 assigned negative charge : -427.2332 centred at (gu) : 100.3827 96.52781 73.14486 start vw surface at 0.1300000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 160629 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32075 grid for indexing accessible points = 1.400000 m= 72067 mr = 105158 m= 22350 mr = 53752 m= 3940 mr = 16026 m= 337 mr = 2404 m= 11 mr = 174 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.520000 number of dielectric boundary points 81820 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 22293 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) : 1.715635 object centre at (A) : 9.952501 17.02950 25.03550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1513715 0.1126692 midg,1,midg; midg,igrid,midg 0.4814952 5.8653373E-03 1,midg,midg; igrid,midg,midg -0.7153199 -0.1353541 gauss-seidel spectral radius is 0.9992037 estimated iterations to convergence 280 setup time was (sec) 1.890000 now iterating at: 10:37:11 rms-change max change #iterations 9.381894 340.9684 at 10iterations 5.518253 162.7246 at 20iterations 3.194599 82.27629 at 30iterations 1.840136 45.59312 at 40iterations 1.049382 29.23904 at 50iterations 0.5988345 13.32699 at 60iterations 0.3406563 8.544466 at 70iterations 0.1934315 4.565076 at 80iterations 0.1095268 2.665702 at 90iterations 6.1766561E-02 1.445438 at 100iterations 3.4955900E-02 0.7507315 at 110iterations 1.9715268E-02 0.4604301 at 120iterations 1.1118240E-02 0.2317286 at 130iterations 6.2633338E-03 0.1265554 at 140iterations 3.5350153E-03 7.1106911E-02 at 150iterations 1.9924541E-03 4.0641785E-02 at 160iterations 1.1221060E-03 2.2601128E-02 at 170iterations 6.3075958E-04 1.3175011E-02 at 180iterations finished qdiffx linear iterations at : 10:37:30 total time elapsed so far: 20.24000 # loops : 180 mean,max change (kT/e) : 6.3075958E-04 1.3175011E-02 energy calculations done at 20.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.41000 DelPhi exited at 10:37:30 20.418u 0.520s 0:21.27 98.4% 0+0k 0+0io 0pf+0w