Sat Oct 15 15:33:05 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 15 2011 at 15:33:05 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2704 !!! WARNING: HIR 79 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6623009 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): -11.17800 36.97100 ymin,ymax (A): -25.55500 22.69200 zmin,zma (A): -8.352000 45.40000 x,y,z range (A): 48.14900 48.24700 53.75200 scale (grids/A): 0.6623009 object centre (A): 12.89650 -1.431500 18.52400 number of atom coordinates read : 2704 total number of charged atoms : 2557 net assigned charge : 3.514013 assigned positive charge : 412.9798 centred at (gu) : 90.05565 90.14419 91.17960 assigned negative charge : -409.4663 centred at (gu) : 89.75777 89.95621 91.09947 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7927 nv = 96 ne = 84 npr = 55932 no. pairs analyzed = 55932 no. exposed pairs = 3290 no. arc points = 22784 no. surface atoms = 1098 nbur = 1606 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 437 mr = 4510 m= 3 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 57 time to turn everything in is 0.4000000 number of dielectric boundary points 3806 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2211 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 9373 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.5788557E-09 3.4407421E-08 midg,1,midg; midg,igrid,midg -3.2096981E-08 5.1612471E-08 1,midg,midg; igrid,midg,midg -5.8009306E-08 7.4028968E-08 gauss-seidel spectral radius is 0.9881892 estimated iterations to convergence 75 setup time was (sec) 0.7500000 now iterating at: 15:33:06 rms-change max change #iterations 0.1753796 24.69389 at 10iterations 1.8886816E-02 2.517067 at 20iterations 2.0805816E-03 0.2725029 at 30iterations 2.2767120E-04 2.8034210E-02 at 40iterations 2.6567663E-05 3.6659241E-03 at 50iterations finished qdiffx linear iterations at : 15:33:10 total time elapsed so far: 4.800000 # loops : 50 mean,max change (kT/e) : 2.6567663E-05 3.6659241E-03 energy calculations done at 4.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.020000 DelPhi exited at 15:33:11 5.023u 0.437s 0:05.95 91.5% 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 15 2011 at 15:33:11 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2704 !!! WARNING: HIR 79 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.986903 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): -11.17800 36.97100 ymin,ymax (A): -25.55500 22.69200 zmin,zma (A): -8.352000 45.40000 x,y,z range (A): 48.14900 48.24700 53.75200 scale (grids/A): 1.986903 object centre (A): 12.89650 -1.431500 18.52400 number of atom coordinates read : 2704 total number of charged atoms : 2557 net assigned charge : 3.514013 assigned positive charge : 412.9798 centred at (gu) : 90.16631 90.43201 93.53853 assigned negative charge : -409.4663 centred at (gu) : 89.27301 89.86836 93.29831 start vw surface at 0.1600000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 85236 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22784 grid for indexing accessible points = 1.400000 m= 31859 mr = 60668 m= 5202 mr = 23600 m= 355 mr = 3265 m= 9 mr = 141 m= 0 mr = 2 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 1189 time to turn everything in is 0.8800000 number of dielectric boundary points 34985 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 20183 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) : 0.6623009 object centre at (A) : 12.89650 -1.431500 18.52400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6260667E-02 1.3396026E-02 midg,1,midg; midg,igrid,midg -2.0884696E-02 3.1115003E-02 1,midg,midg; igrid,midg,midg -1.6052175E-02 8.1107341E-02 gauss-seidel spectral radius is 0.9987516 estimated iterations to convergence 224 setup time was (sec) 1.230000 now iterating at: 15:33:12 rms-change max change #iterations 4.802573 289.4428 at 10iterations 2.334501 73.68073 at 20iterations 1.128104 33.90848 at 30iterations 0.5463287 19.14611 at 40iterations 0.2654058 7.632226 at 50iterations 0.1284550 3.908520 at 60iterations 6.2293269E-02 1.831080 at 70iterations 3.0319126E-02 0.9943428 at 80iterations 1.4748068E-02 0.4687614 at 90iterations 7.1471538E-03 0.2057800 at 100iterations 3.4787834E-03 0.1125488 at 110iterations 1.6994491E-03 5.3559303E-02 at 120iterations finished qdiffx linear iterations at : 15:33:23 total time elapsed so far: 11.70000 # loops : 120 mean,max change (kT/e) : 1.6994491E-03 5.3559303E-02 energy calculations done at 11.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.92000 DelPhi exited at 15:33:23 11.922u 0.488s 0:12.75 97.2% 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 Sat Oct 15 2011 at 15:33:23 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2704 !!! WARNING: HIR 79 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: 2.980354 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): -11.17800 36.97100 ymin,ymax (A): -25.55500 22.69200 zmin,zma (A): -8.352000 45.40000 x,y,z range (A): 48.14900 48.24700 53.75200 scale (grids/A): 2.980354 object centre (A): 12.89650 -1.431500 18.52400 number of atom coordinates read : 2704 total number of charged atoms : 2557 net assigned charge : 3.514013 assigned positive charge : 412.9798 centred at (gu) : 90.24926 90.64798 95.30770 assigned negative charge : -409.4663 centred at (gu) : 88.90948 89.80254 94.94746 start vw surface at 0.1600000 fill in re-entrant regions at 0.7600000 boundary points on vw surface= 196779 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22784 grid for indexing accessible points = 1.400000 m= 102271 mr = 145881 m= 37948 mr = 84527 m= 9458 mr = 30690 m= 1457 mr = 7027 m= 109 mr = 963 m= 3 mr = 64 m= 0 mr = 2 time to grow re-entrant surface = 1.420000 no. cavity mid-points inaccessible to solvent = 3712 time to turn everything in is 2.330000 number of dielectric boundary points 78871 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.500000 number of grid points assigned charge 20456 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) : 1.986903 object centre at (A) : 12.89650 -1.431500 18.52400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3289598 0.3520432 midg,1,midg; midg,igrid,midg -0.2216287 0.3696886 1,midg,midg; igrid,midg,midg -7.0985876E-02 0.6744778 gauss-seidel spectral radius is 0.9992845 estimated iterations to convergence 295 setup time was (sec) 2.740000 now iterating at: 15:33:27 rms-change max change #iterations 10.93719 390.1177 at 10iterations 6.422323 148.6089 at 20iterations 3.764930 67.78325 at 30iterations 2.200597 41.33457 at 40iterations 1.286421 28.88697 at 50iterations 0.7507997 13.49230 at 60iterations 0.4370309 7.487450 at 70iterations 0.2551986 4.104420 at 80iterations 0.1486349 2.603776 at 90iterations 8.6321436E-02 1.443306 at 100iterations 5.0302673E-02 0.9719667 at 110iterations 2.9287091E-02 0.4685097 at 120iterations 1.7081687E-02 0.3025084 at 130iterations 9.9361576E-03 0.1673241 at 140iterations 5.8270320E-03 9.8943710E-02 at 150iterations 3.4289355E-03 5.6570053E-02 at 160iterations 2.0329375E-03 3.5092354E-02 at 170iterations 1.2280775E-03 2.2024632E-02 at 180iterations finished qdiffx linear iterations at : 15:33:56 total time elapsed so far: 20.87000 # loops : 180 mean,max change (kT/e) : 1.2280775E-03 2.2024632E-02 energy calculations done at 20.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.10000 DelPhi exited at 15:33:58 21.103u 0.674s 0:34.56 62.9% 0+0k 0+0io 0pf+0w