Sun Oct 9 00:35:55 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 Sun Oct 9 2011 at 00:35:55 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2890 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: ARG 297 has a net charge of -0.2720 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5859407 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): 47.86800 94.01100 ymin,ymax (A): 22.68200 83.43900 zmin,zma (A): -14.10900 41.01300 x,y,z range (A): 46.14300 60.75700 55.12199 scale (grids/A): 0.5859407 object centre (A): 70.93950 53.06050 13.45200 number of atom coordinates read : 2890 total number of charged atoms : 2747 net assigned charge : 3.968035 assigned positive charge : 425.0214 centred at (gu) : 90.87606 89.42384 88.25021 assigned negative charge : -421.0546 centred at (gu) : 90.75999 89.27397 88.14263 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6712 nv = 96 ne = 84 npr = 57903 no. pairs analyzed = 57903 no. exposed pairs = 3668 no. arc points = 25718 no. surface atoms = 1222 nbur = 1668 mkacc time = 0.1000000 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 = 1.456000 m= 340 mr = 3610 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.2100000 number of dielectric boundary points 3420 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2575 ## 273 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8435 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5144500E-09 2.5345708E-09 midg,1,midg; midg,igrid,midg -3.1406586E-09 4.2216994E-09 1,midg,midg; igrid,midg,midg -1.4985263E-09 4.9128137E-09 gauss-seidel spectral radius is 0.9849617 estimated iterations to convergence 67 setup time was (sec) 0.4000000 now iterating at: 00:35:56 rms-change max change #iterations 0.1039529 15.54114 at 10iterations 8.2183015E-03 1.228383 at 20iterations 6.5493351E-04 0.1014669 at 30iterations 5.3575055E-05 7.8287125E-03 at 40iterations 4.3607320E-06 7.8964233E-04 at 50iterations finished qdiffx linear iterations at : 00:35:59 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 4.3607320E-06 7.8964233E-04 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 00:35:59 3.371u 0.172s 0:03.84 92.1% 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 Sun Oct 9 2011 at 00:35:59 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2890 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: ARG 297 has a net charge of -0.2720 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.757822 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): 47.86800 94.01100 ymin,ymax (A): 22.68200 83.43900 zmin,zma (A): -14.10900 41.01300 x,y,z range (A): 46.14300 60.75700 55.12199 scale (grids/A): 1.757822 object centre (A): 70.93950 53.06050 13.45200 number of atom coordinates read : 2890 total number of charged atoms : 2747 net assigned charge : 3.968035 assigned positive charge : 425.0214 centred at (gu) : 92.62735 88.27078 84.74995 assigned negative charge : -421.0546 centred at (gu) : 92.27989 87.82184 84.42787 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 74098 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25718 grid for indexing accessible points = 1.400000 m= 25180 mr = 51188 m= 3261 mr = 17997 m= 158 mr = 1814 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 750 time to turn everything in is 0.3600000 number of dielectric boundary points 31658 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 227 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 21388 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) : 0.5859407 object centre at (A) : 70.93950 53.06050 13.45200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.6189173E-03 2.9449277E-02 midg,1,midg; midg,igrid,midg 2.4351119E-03 2.4638470E-02 1,midg,midg; igrid,midg,midg -9.7610746E-03 5.0275987E-03 gauss-seidel spectral radius is 0.9984316 estimated iterations to convergence 200 setup time was (sec) 0.5800000 now iterating at: 00:36:00 rms-change max change #iterations 3.784162 157.6780 at 10iterations 1.668966 74.74225 at 20iterations 0.7374763 24.19934 at 30iterations 0.3279169 11.97268 at 40iterations 0.1450252 5.801067 at 50iterations 6.4418934E-02 2.127618 at 60iterations 2.8430788E-02 1.047426 at 70iterations 1.2620807E-02 0.4337873 at 80iterations 5.6059044E-03 0.2061768 at 90iterations 2.4909002E-03 8.2422256E-02 at 100iterations 1.1063108E-03 3.6303520E-02 at 110iterations 4.8944814E-04 1.8501282E-02 at 120iterations finished qdiffx linear iterations at : 00:36:07 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 4.8944814E-04 1.8501282E-02 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 00:36:08 7.755u 0.187s 0:08.29 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 Sun Oct 9 2011 at 00:36:08 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2890 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: ARG 297 has a net charge of -0.2720 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.636733 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): 47.86800 94.01100 ymin,ymax (A): 22.68200 83.43900 zmin,zma (A): -14.10900 41.01300 x,y,z range (A): 46.14300 60.75700 55.12199 scale (grids/A): 2.636733 object centre (A): 70.93950 53.06050 13.45200 number of atom coordinates read : 2890 total number of charged atoms : 2747 net assigned charge : 3.968035 assigned positive charge : 425.0214 centred at (gu) : 93.94090 87.40600 82.12485 assigned negative charge : -421.0546 centred at (gu) : 93.41972 86.73272 81.64183 start vw surface at 0.1000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 171493 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25718 grid for indexing accessible points = 1.400000 m= 84126 mr = 124561 m= 27549 mr = 67707 m= 5565 mr = 21511 m= 629 mr = 3858 m= 17 mr = 335 m= 0 mr = 6 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 2349 time to turn everything in is 0.9000000 number of dielectric boundary points 71401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 21946 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) : 1.757822 object centre at (A) : 70.93950 53.06050 13.45200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1455197 0.5304089 midg,1,midg; midg,igrid,midg 0.1877211 0.2625377 1,midg,midg; igrid,midg,midg -7.9764619E-02 7.2080843E-02 gauss-seidel spectral radius is 0.9992103 estimated iterations to convergence 281 setup time was (sec) 1.130000 now iterating at: 00:36:09 rms-change max change #iterations 9.400469 291.8846 at 10iterations 5.415416 126.2272 at 20iterations 3.094496 64.02280 at 30iterations 1.757690 41.88226 at 40iterations 0.9986163 20.65054 at 50iterations 0.5657216 11.95613 at 60iterations 0.3188975 6.706410 at 70iterations 0.1800931 3.245325 at 80iterations 0.1017972 2.079826 at 90iterations 5.7387073E-02 1.117871 at 100iterations 3.2315496E-02 0.6013489 at 110iterations 1.8232191E-02 0.3870018 at 120iterations 1.0271793E-02 0.1893196 at 130iterations 5.7960423E-03 0.1112404 at 140iterations 3.2600176E-03 6.0211182E-02 at 150iterations 1.8376901E-03 3.6608696E-02 at 160iterations 1.0378992E-03 1.8728256E-02 at 170iterations 5.8449939E-04 1.0373592E-02 at 180iterations finished qdiffx linear iterations at : 00:36:20 total time elapsed so far: 12.43000 # loops : 180 mean,max change (kT/e) : 5.8449939E-04 1.0373592E-02 energy calculations done at 12.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.56000 DelPhi exited at 00:36:21 12.563u 0.216s 0:13.21 96.6% 0+0k 0+0io 0pf+0w