Sun Oct 9 15:00:16 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 15:00:16 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1137 !!! WARNING: HIR 87 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.8724849 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): 11.40800 52.21100 ymin,ymax (A): -52.70700 -16.92400 zmin,zma (A): -66.88700 -29.32900 x,y,z range (A): 40.80300 35.78300 37.55800 scale (grids/A): 0.8724849 object centre (A): 31.80950 -34.81550 -48.10800 number of atom coordinates read : 1137 total number of charged atoms : 1009 net assigned charge : 2.514006 assigned positive charge : 164.4092 centred at (gu) : 90.76460 88.28226 90.22466 assigned negative charge : -161.8951 centred at (gu) : 90.39930 88.16756 90.10758 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6199 nv = 96 ne = 84 npr = 23641 no. pairs analyzed = 23641 no. exposed pairs = 1480 no. arc points = 10614 no. surface atoms = 500 nbur = 637 mkacc time = 5.9999987E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 522 mr = 3426 m= 3 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 53 time to turn everything in is 0.2200000 number of dielectric boundary points 3173 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 574 ## 63 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 5207 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.6715197E-08 1.1382192E-06 midg,1,midg; midg,igrid,midg -1.2002060E-07 8.2634472E-07 1,midg,midg; igrid,midg,midg -1.2321032E-06 2.6179491E-06 gauss-seidel spectral radius is 0.9930373 estimated iterations to convergence 97 setup time was (sec) 0.4400000 now iterating at: 15:00:17 rms-change max change #iterations 0.3207126 49.74030 at 10iterations 5.7789378E-02 7.623863 at 20iterations 1.0322894E-02 1.582703 at 30iterations 1.8560962E-03 0.2440128 at 40iterations 3.2974491E-04 4.2083740E-02 at 50iterations finished qdiffx linear iterations at : 15:00:19 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 3.2974491E-04 4.2083740E-02 energy calculations done at 3.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 15:00:20 3.274u 0.165s 0:03.78 90.7% 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 Sun Oct 9 2011 at 15:00:20 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1137 !!! WARNING: HIR 87 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: 2.617455 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): 11.40800 52.21100 ymin,ymax (A): -52.70700 -16.92400 zmin,zma (A): -66.88700 -29.32900 x,y,z range (A): 40.80300 35.78300 37.55800 scale (grids/A): 2.617455 object centre (A): 31.80950 -34.81550 -48.10800 number of atom coordinates read : 1137 total number of charged atoms : 1009 net assigned charge : 2.514006 assigned positive charge : 164.4092 centred at (gu) : 92.29408 84.84708 90.67406 assigned negative charge : -161.8951 centred at (gu) : 91.19806 84.50267 90.32284 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 63308 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10614 grid for indexing accessible points = 1.400000 m= 27412 mr = 43124 m= 6796 mr = 21149 m= 995 mr = 4822 m= 76 mr = 642 m= 3 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1574 time to turn everything in is 0.5500000 number of dielectric boundary points 28811 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 8067 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) : 0.8724849 object centre at (A) : 31.80950 -34.81550 -48.10800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6662439E-02 2.0557445E-02 midg,1,midg; midg,igrid,midg -9.8789344E-03 3.6329456E-02 1,midg,midg; igrid,midg,midg -7.0708811E-02 0.1565666 gauss-seidel spectral radius is 0.9990867 estimated iterations to convergence 261 setup time was (sec) 0.8400000 now iterating at: 15:00:21 rms-change max change #iterations 4.639393 238.3495 at 10iterations 2.496578 98.87796 at 20iterations 1.337417 47.21970 at 30iterations 0.7181275 20.84139 at 40iterations 0.3850437 12.42878 at 50iterations 0.2073174 6.718028 at 60iterations 0.1110726 3.509087 at 70iterations 5.9650555E-02 1.903900 at 80iterations 3.2240774E-02 0.9466209 at 90iterations 1.7214106E-02 0.5377789 at 100iterations 9.2186527E-03 0.2725163 at 110iterations 4.9660499E-03 0.1453171 at 120iterations finished qdiffx linear iterations at : 15:00:27 total time elapsed so far: 7.270000 # loops : 120 mean,max change (kT/e) : 4.9660499E-03 0.1453171 energy calculations done at 7.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.450000 DelPhi exited at 15:00:28 7.453u 0.160s 0:07.91 96.2% 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 15:00:28 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1137 !!! WARNING: HIR 87 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.926182 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): 11.40800 52.21100 ymin,ymax (A): -52.70700 -16.92400 zmin,zma (A): -66.88700 -29.32900 x,y,z range (A): 40.80300 35.78300 37.55800 scale (grids/A): 3.926182 object centre (A): 31.80950 -34.81550 -48.10800 number of atom coordinates read : 1137 total number of charged atoms : 1009 net assigned charge : 2.514006 assigned positive charge : 164.4092 centred at (gu) : 93.44125 82.27064 91.01115 assigned negative charge : -161.8951 centred at (gu) : 91.79710 81.75404 90.48433 start vw surface at 0.1200000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 145139 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10614 grid for indexing accessible points = 1.400000 m= 80598 mr = 103214 m= 38316 mr = 67522 m= 13460 mr = 32240 m= 3680 mr = 10732 m= 786 mr = 2894 m= 134 mr = 580 m= 17 mr = 106 m= 0 mr = 14 time to grow re-entrant surface = 0.8099999 no. cavity mid-points inaccessible to solvent = 4899 time to turn everything in is 1.690000 number of dielectric boundary points 64828 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 8072 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) : 2.617455 object centre at (A) : 31.80950 -34.81550 -48.10800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2062627 0.1215284 midg,1,midg; midg,igrid,midg -0.2043707 0.1267875 1,midg,midg; igrid,midg,midg -0.7457056 1.342355 gauss-seidel spectral radius is 0.9993409 estimated iterations to convergence 307 setup time was (sec) 1.980000 now iterating at: 15:00:30 rms-change max change #iterations 9.494700 223.8452 at 10iterations 5.639609 118.2386 at 20iterations 3.349772 67.56123 at 30iterations 1.986689 34.17497 at 40iterations 1.181594 20.25719 at 50iterations 0.6999032 12.70021 at 60iterations 0.4148391 7.654919 at 70iterations 0.2459623 4.103049 at 80iterations 0.1460930 2.537315 at 90iterations 8.6360969E-02 1.521811 at 100iterations 5.1284179E-02 0.8730898 at 110iterations 3.0394021E-02 0.5435953 at 120iterations 1.8036786E-02 0.3227177 at 130iterations 1.0659923E-02 0.1917725 at 140iterations 6.3161058E-03 0.1097050 at 150iterations 3.7447398E-03 6.7714691E-02 at 160iterations 2.2202351E-03 3.9234161E-02 at 170iterations 1.3172559E-03 2.2073746E-02 at 180iterations finished qdiffx linear iterations at : 15:00:40 total time elapsed so far: 12.06000 # loops : 180 mean,max change (kT/e) : 1.3172559E-03 2.2073746E-02 energy calculations done at 12.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.24000 DelPhi exited at 15:00:41 12.245u 0.194s 0:12.71 97.7% 0+0k 0+0io 0pf+0w