Sun Oct 9 11:25:48 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+sph.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 = amb.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 11:25:48 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1879 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7475379 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): -1.324000 44.68600 ymin,ymax (A): -21.18500 23.85300 zmin,zma (A): -7.977000 39.64600 x,y,z range (A): 46.01000 45.03800 47.62300 scale (grids/A): 0.7475379 object centre (A): 21.68100 1.334000 15.83450 number of atom coordinates read : 1879 total number of charged atoms : 1743 net assigned charge : -6.499981 assigned positive charge : 275.6360 centred at (gu) : 89.79867 90.02938 89.85489 assigned negative charge : -282.1361 centred at (gu) : 89.78526 89.96677 89.72466 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 7290 nv = 96 ne = 84 npr = 39475 no. pairs analyzed = 39475 no. exposed pairs = 2211 no. arc points = 15794 no. surface atoms = 754 nbur = 1125 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 499 mr = 4141 m= 5 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 152 time to turn everything in is 0.1600000 number of dielectric boundary points 3565 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1288 ## 104 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7546 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7930679E-07 -4.0023868E-10 midg,1,midg; midg,igrid,midg -1.9900922E-07 -6.9775901E-08 1,midg,midg; igrid,midg,midg -1.5384418E-07 -1.1618254E-07 gauss-seidel spectral radius is 0.9906496 estimated iterations to convergence 84 setup time was (sec) 0.3600000 now iterating at: 11:25:48 rms-change max change #iterations 0.2497192 32.64553 at 10iterations 3.4252763E-02 5.281055 at 20iterations 4.6579232E-03 0.6478539 at 30iterations 6.4278144E-04 9.9813461E-02 at 40iterations 8.7902998E-05 1.2363434E-02 at 50iterations finished qdiffx linear iterations at : 11:25:51 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 8.7902998E-05 1.2363434E-02 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 11:25:52 3.569u 0.205s 0:04.06 92.6% 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 11:25:52 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1879 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.242614 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): -1.324000 44.68600 ymin,ymax (A): -21.18500 23.85300 zmin,zma (A): -7.977000 39.64600 x,y,z range (A): 46.01000 45.03800 47.62300 scale (grids/A): 2.242614 object centre (A): 21.68100 1.334000 15.83450 number of atom coordinates read : 1879 total number of charged atoms : 1743 net assigned charge : -6.499981 assigned positive charge : 275.6360 centred at (gu) : 89.39602 90.08838 89.56481 assigned negative charge : -282.1361 centred at (gu) : 89.35578 89.90051 89.17402 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 76547 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15794 grid for indexing accessible points = 1.400000 m= 31395 mr = 53743 m= 6818 mr = 24157 m= 698 mr = 4637 m= 25 mr = 342 m= 0 mr = 1 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 4374 time to turn everything in is 0.4000000 number of dielectric boundary points 32603 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 39 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 13890 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) : 0.7475379 object centre at (A) : 21.68100 1.334000 15.83450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1442391 -3.6166251E-02 midg,1,midg; midg,igrid,midg 4.6727275E-03 2.7848275E-02 1,midg,midg; igrid,midg,midg -5.1903203E-02 -4.0141955E-02 gauss-seidel spectral radius is 0.9989208 estimated iterations to convergence 241 setup time was (sec) 0.6400000 now iterating at: 11:25:53 rms-change max change #iterations 4.819662 218.2463 at 10iterations 2.442437 82.45595 at 20iterations 1.241484 38.75124 at 30iterations 0.6351678 19.16862 at 40iterations 0.3233447 9.123596 at 50iterations 0.1645160 4.890556 at 60iterations 8.3808757E-02 2.382813 at 70iterations 4.2735603E-02 1.244878 at 80iterations 2.1760704E-02 0.6551590 at 90iterations 1.1102980E-02 0.3447571 at 100iterations 5.6410935E-03 0.1694984 at 110iterations 2.8778890E-03 8.7869644E-02 at 120iterations finished qdiffx linear iterations at : 11:26:00 total time elapsed so far: 8.240000 # loops : 120 mean,max change (kT/e) : 2.8778890E-03 8.7869644E-02 energy calculations done at 8.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.370000 DelPhi exited at 11:26:01 8.369u 0.243s 0:09.00 95.5% 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 Sun Oct 9 2011 at 11:26:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1879 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.363921 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): -1.324000 44.68600 ymin,ymax (A): -21.18500 23.85300 zmin,zma (A): -7.977000 39.64600 x,y,z range (A): 46.01000 45.03800 47.62300 scale (grids/A): 3.363921 object centre (A): 21.68100 1.334000 15.83450 number of atom coordinates read : 1879 total number of charged atoms : 1743 net assigned charge : -6.499981 assigned positive charge : 275.6360 centred at (gu) : 89.09409 90.13277 89.34728 assigned negative charge : -282.1361 centred at (gu) : 89.03367 89.85083 88.76105 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 176123 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15794 grid for indexing accessible points = 1.400000 m= 95659 mr = 129134 m= 41766 mr = 80217 m= 13202 mr = 34620 m= 2860 mr = 10341 m= 348 mr = 2078 m= 15 mr = 208 m= 0 mr = 1 time to grow re-entrant surface = 0.6100001 no. cavity mid-points inaccessible to solvent = 15443 time to turn everything in is 1.220000 number of dielectric boundary points 73374 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 13944 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) : 2.242614 object centre at (A) : 21.68100 1.334000 15.83450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.363195 -0.2504360 midg,1,midg; midg,igrid,midg 8.3777063E-02 0.2536485 1,midg,midg; igrid,midg,midg -0.3608010 -0.3647695 gauss-seidel spectral radius is 0.9993152 estimated iterations to convergence 301 setup time was (sec) 1.460000 now iterating at: 11:26:03 rms-change max change #iterations 10.39150 309.5518 at 10iterations 6.155552 135.5625 at 20iterations 3.628969 70.34230 at 30iterations 2.135041 37.33408 at 40iterations 1.255076 27.36266 at 50iterations 0.7400091 12.22532 at 60iterations 0.4349712 7.805823 at 70iterations 0.2555770 4.328621 at 80iterations 0.1502694 2.658989 at 90iterations 8.7983191E-02 1.407604 at 100iterations 5.1697902E-02 0.8351765 at 110iterations 3.0369155E-02 0.5086823 at 120iterations 1.7855670E-02 0.3250656 at 130iterations 1.0488759E-02 0.1781181 at 140iterations 6.1399196E-03 0.1023750 at 150iterations 3.6141155E-03 6.0310364E-02 at 160iterations 2.1140804E-03 3.4984589E-02 at 170iterations 1.2440474E-03 1.9765854E-02 at 180iterations finished qdiffx linear iterations at : 11:26:15 total time elapsed so far: 13.28000 # loops : 180 mean,max change (kT/e) : 1.2440474E-03 1.9765854E-02 energy calculations done at 13.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.41000 DelPhi exited at 11:26:15 13.415u 0.222s 0:14.02 97.2% 0+0k 0+0io 0pf+0w