Sun Oct 9 23:14:32 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 23:14:32 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 = 2339 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: 0.6572631 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): -11.81400 31.34100 ymin,ymax (A): -22.34300 31.82100 zmin,zma (A): -9.976000 43.33100 x,y,z range (A): 43.15500 54.16400 53.30700 scale (grids/A): 0.6572631 object centre (A): 9.763500 4.739000 16.67750 number of atom coordinates read : 2339 total number of charged atoms : 2199 net assigned charge : 5.500006 assigned positive charge : 350.9805 centred at (gu) : 92.04786 90.43600 89.80723 assigned negative charge : -345.4807 centred at (gu) : 91.95717 90.31693 89.63718 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6932 nv = 96 ne = 84 npr = 45970 no. pairs analyzed = 45970 no. exposed pairs = 2947 no. arc points = 20995 no. surface atoms = 1009 nbur = 1330 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 386 mr = 3746 m= 4 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3526 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2003 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8023 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6408260E-08 3.8317577E-08 midg,1,midg; midg,igrid,midg -6.4296075E-09 3.4845190E-08 1,midg,midg; igrid,midg,midg -1.3414823E-09 4.1947033E-08 gauss-seidel spectral radius is 0.9879851 estimated iterations to convergence 74 setup time was (sec) 0.5200000 now iterating at: 23:14:33 rms-change max change #iterations 0.1612833 22.50025 at 10iterations 1.6977374E-02 2.781679 at 20iterations 1.7838989E-03 0.2512331 at 30iterations 2.6921535E-04 4.7359943E-02 at 40iterations 8.9492118E-05 1.7060757E-02 at 50iterations finished qdiffx linear iterations at : 23:14:35 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 8.9492118E-05 1.7060757E-02 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 23:14:36 3.173u 0.153s 0:03.72 89.2% 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 23:14:36 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 = 2339 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: 1.971789 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): -11.81400 31.34100 ymin,ymax (A): -22.34300 31.82100 zmin,zma (A): -9.976000 43.33100 x,y,z range (A): 43.15500 54.16400 53.30700 scale (grids/A): 1.971789 object centre (A): 9.763500 4.739000 16.67750 number of atom coordinates read : 2339 total number of charged atoms : 2199 net assigned charge : 5.500006 assigned positive charge : 350.9805 centred at (gu) : 96.14321 91.30781 89.42127 assigned negative charge : -345.4807 centred at (gu) : 95.87133 90.95059 88.91150 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74744 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20995 grid for indexing accessible points = 1.400000 m= 26436 mr = 51178 m= 4335 mr = 19299 m= 292 mr = 2779 m= 1 mr = 129 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 32423 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 17334 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) : 0.6572631 object centre at (A) : 9.763500 4.739000 16.67750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1007437E-02 1.2099682E-02 midg,1,midg; midg,igrid,midg 1.7929450E-02 2.7041884E-02 1,midg,midg; igrid,midg,midg -8.6980900E-03 8.7444363E-03 gauss-seidel spectral radius is 0.9987022 estimated iterations to convergence 220 setup time was (sec) 0.8000000 now iterating at: 23:14:37 rms-change max change #iterations 4.259982 169.4728 at 10iterations 2.035794 77.52341 at 20iterations 0.9738342 33.32794 at 30iterations 0.4647627 14.02352 at 40iterations 0.2212913 8.576519 at 50iterations 0.1062422 3.494785 at 60iterations 5.0571419E-02 1.786098 at 70iterations 2.4153346E-02 0.7155092 at 80iterations 1.1542175E-02 0.3456783 at 90iterations 5.5230935E-03 0.1985264 at 100iterations 2.6504179E-03 9.2697144E-02 at 110iterations 1.2804748E-03 4.3318748E-02 at 120iterations finished qdiffx linear iterations at : 23:14:43 total time elapsed so far: 7.300000 # loops : 120 mean,max change (kT/e) : 1.2804748E-03 4.3318748E-02 energy calculations done at 7.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.470000 DelPhi exited at 23:14:44 7.469u 0.180s 0:07.93 96.3% 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 23:14:44 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 = 2339 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: 2.957684 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): -11.81400 31.34100 ymin,ymax (A): -22.34300 31.82100 zmin,zma (A): -9.976000 43.33100 x,y,z range (A): 43.15500 54.16400 53.30700 scale (grids/A): 2.957684 object centre (A): 9.763500 4.739000 16.67750 number of atom coordinates read : 2339 total number of charged atoms : 2199 net assigned charge : 5.500006 assigned positive charge : 350.9805 centred at (gu) : 99.21484 91.96169 89.13184 assigned negative charge : -345.4807 centred at (gu) : 98.80703 91.42571 88.36724 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 172513 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20995 grid for indexing accessible points = 1.400000 m= 86152 mr = 124065 m= 30730 mr = 70099 m= 7969 mr = 24481 m= 1331 mr = 6074 m= 103 mr = 950 m= 2 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.310000 number of dielectric boundary points 73073 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 17591 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) : 1.971789 object centre at (A) : 9.763500 4.739000 16.67750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1074658 -3.4192268E-02 midg,1,midg; midg,igrid,midg 0.3520900 0.1230187 1,midg,midg; igrid,midg,midg -0.1601498 5.9735183E-02 gauss-seidel spectral radius is 0.9992766 estimated iterations to convergence 293 setup time was (sec) 1.590000 now iterating at: 23:14:45 rms-change max change #iterations 9.957896 308.9297 at 10iterations 5.873257 208.2568 at 20iterations 3.442815 97.63862 at 30iterations 2.016098 40.19458 at 40iterations 1.175931 24.57808 at 50iterations 0.6839580 14.26898 at 60iterations 0.3976681 7.474945 at 70iterations 0.2315863 4.315937 at 80iterations 0.1342397 2.476247 at 90iterations 7.7851653E-02 1.476182 at 100iterations 4.5191426E-02 0.8244528 at 110iterations 2.6191320E-02 0.5201550 at 120iterations 1.5131772E-02 0.2637100 at 130iterations 8.7804189E-03 0.1558552 at 140iterations 5.0853170E-03 8.8416576E-02 at 150iterations 2.9449721E-03 5.8073044E-02 at 160iterations 1.7083635E-03 2.9561996E-02 at 170iterations 9.9252688E-04 1.7971039E-02 at 180iterations finished qdiffx linear iterations at : 23:14:55 total time elapsed so far: 11.37000 # loops : 180 mean,max change (kT/e) : 9.9252688E-04 1.7971039E-02 energy calculations done at 11.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.55000 DelPhi exited at 23:14:56 11.549u 0.202s 0:12.11 96.9% 0+0k 0+0io 0pf+0w