Sat Oct 15 12:08:41 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 12:08:41 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2266 !!! WARNING: HIT 84 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: 0.6360664 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): -5.4000020E-02 52.83100 ymin,ymax (A): -16.43300 27.41500 zmin,zma (A): 28.55900 84.52800 x,y,z range (A): 52.88500 43.84800 55.96900 scale (grids/A): 0.6360664 object centre (A): 26.38850 5.491000 56.54350 number of atom coordinates read : 2266 total number of charged atoms : 2132 net assigned charge : 10.01402 assigned positive charge : 332.2726 centred at (gu) : 90.78333 89.49836 89.30918 assigned negative charge : -322.2592 centred at (gu) : 90.77196 89.58561 89.29374 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6365 nv = 96 ne = 84 npr = 44887 no. pairs analyzed = 44887 no. exposed pairs = 3018 no. arc points = 22088 no. surface atoms = 1005 nbur = 1261 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 352 mr = 3286 m= 0 mr = 37 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3394 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2150 ## 196 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7511 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3403768E-08 1.2387333E-08 midg,1,midg; midg,igrid,midg 2.2774206E-08 4.8244773E-09 1,midg,midg; igrid,midg,midg 1.0189555E-08 1.6435548E-08 gauss-seidel spectral radius is 0.9871773 estimated iterations to convergence 72 setup time was (sec) 0.3700000 now iterating at: 12:08:41 rms-change max change #iterations 0.1308128 21.18738 at 10iterations 1.2687636E-02 1.924917 at 20iterations 1.2350687E-03 0.1976147 at 30iterations 1.3088525E-04 2.0824432E-02 at 40iterations 1.7043034E-05 2.8195381E-03 at 50iterations finished qdiffx linear iterations at : 12:08:44 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 1.7043034E-05 2.8195381E-03 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 12:08:45 3.473u 0.209s 0:04.13 88.8% 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 12:08:45 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2266 !!! WARNING: HIT 84 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: 1.908199 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): -5.4000020E-02 52.83100 ymin,ymax (A): -16.43300 27.41500 zmin,zma (A): 28.55900 84.52800 x,y,z range (A): 52.88500 43.84800 55.96900 scale (grids/A): 1.908199 object centre (A): 26.38850 5.491000 56.54350 number of atom coordinates read : 2266 total number of charged atoms : 2132 net assigned charge : 10.01402 assigned positive charge : 332.2726 centred at (gu) : 92.34998 88.49500 87.92754 assigned negative charge : -322.2592 centred at (gu) : 92.31606 88.75704 87.88139 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 67988 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22088 grid for indexing accessible points = 1.400000 m= 24135 mr = 45130 m= 3862 mr = 17224 m= 244 mr = 2305 m= 3 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 31487 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 16793 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) : 0.6360664 object centre at (A) : 26.38850 5.491000 56.54350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7473031E-02 3.3355553E-02 midg,1,midg; midg,igrid,midg 2.5184702E-02 -3.0663060E-03 1,midg,midg; igrid,midg,midg 3.8062617E-02 4.2400833E-02 gauss-seidel spectral radius is 0.9986195 estimated iterations to convergence 213 setup time was (sec) 0.5700000 now iterating at: 12:08:46 rms-change max change #iterations 3.857698 176.5166 at 10iterations 1.795791 69.39457 at 20iterations 0.8356763 31.79119 at 30iterations 0.3858136 13.51442 at 40iterations 0.1801471 6.874002 at 50iterations 8.3926201E-02 2.959722 at 60iterations 3.9015450E-02 1.454594 at 70iterations 1.8190984E-02 0.6002197 at 80iterations 8.4751984E-03 0.2850552 at 90iterations 3.9348085E-03 0.1283994 at 100iterations 1.8291456E-03 6.0008049E-02 at 110iterations 8.5638877E-04 2.8841019E-02 at 120iterations finished qdiffx linear iterations at : 12:08:53 total time elapsed so far: 7.920000 # loops : 120 mean,max change (kT/e) : 8.5638877E-04 2.8841019E-02 energy calculations done at 7.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.050000 DelPhi exited at 12:08:53 8.056u 0.221s 0:08.68 95.2% 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 12:08:54 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2266 !!! WARNING: HIT 84 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: 2.862299 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): -5.4000020E-02 52.83100 ymin,ymax (A): -16.43300 27.41500 zmin,zma (A): 28.55900 84.52800 x,y,z range (A): 52.88500 43.84800 55.96900 scale (grids/A): 2.862299 object centre (A): 26.38850 5.491000 56.54350 number of atom coordinates read : 2266 total number of charged atoms : 2132 net assigned charge : 10.01402 assigned positive charge : 332.2726 centred at (gu) : 93.52488 87.74242 86.89127 assigned negative charge : -322.2592 centred at (gu) : 93.47408 88.13561 86.82207 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 157124 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22088 grid for indexing accessible points = 1.400000 m= 77241 mr = 109874 m= 28235 mr = 61838 m= 6930 mr = 22106 m= 1058 mr = 5055 m= 42 mr = 709 m= 0 mr = 14 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8600000 number of dielectric boundary points 71034 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 17056 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) : 1.908199 object centre at (A) : 26.38850 5.491000 56.54350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3379615 0.6168367 midg,1,midg; midg,igrid,midg 0.2445947 -3.4857266E-02 1,midg,midg; igrid,midg,midg 0.4054128 0.4054154 gauss-seidel spectral radius is 0.9992598 estimated iterations to convergence 290 setup time was (sec) 1.100000 now iterating at: 12:08:55 rms-change max change #iterations 9.270233 354.4154 at 10iterations 5.459490 137.3706 at 20iterations 3.167496 72.20879 at 30iterations 1.841003 41.67838 at 40iterations 1.068328 21.50764 at 50iterations 0.6170198 13.22819 at 60iterations 0.3557607 7.320608 at 70iterations 0.2054920 4.551985 at 80iterations 0.1181978 2.098000 at 90iterations 6.7990206E-02 1.277428 at 100iterations 3.9188791E-02 0.7856674 at 110iterations 2.2507949E-02 0.4336052 at 120iterations 1.2940931E-02 0.2595005 at 130iterations 7.4415789E-03 0.1408691 at 140iterations 4.2715361E-03 8.9014530E-02 at 150iterations 2.4536217E-03 5.3112030E-02 at 160iterations 1.4124601E-03 2.9940605E-02 at 170iterations 8.1367965E-04 1.6361237E-02 at 180iterations finished qdiffx linear iterations at : 12:09:07 total time elapsed so far: 12.96000 # loops : 180 mean,max change (kT/e) : 8.1367965E-04 1.6361237E-02 energy calculations done at 12.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.09000 DelPhi exited at 12:09:07 13.091u 0.257s 0:13.65 97.7% 0+0k 0+0io 0pf+0w