Wed Feb 15 08:56:58 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:56:58 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3338 !!! WARNING: HID 15 has a net charge of 1.4000 !!! WARNING: HID 17 has a net charge of 1.4000 !!! WARNING: ZN5 522 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6323044 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): 32.08200 81.47400 ymin,ymax (A): 25.28900 81.59100 zmin,zma (A): -2.982000 46.36000 x,y,z range (A): 49.39200 56.30199 49.34200 scale (grids/A): 0.6323044 object centre (A): 56.77800 53.44000 21.68900 number of atom coordinates read : 3338 total number of charged atoms : 3165 net assigned charge : -0.2999887 assigned positive charge : 507.4063 centred at (gu) : 90.84971 89.61575 91.09287 assigned negative charge : -507.7076 centred at (gu) : 90.62971 89.71898 91.06792 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8590 nv = 96 ne = 84 npr = 71813 no. pairs analyzed = 71813 no. exposed pairs = 3708 no. arc points = 25198 no. surface atoms = 1274 nbur = 2064 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 487 mr = 5134 m= 3 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.3900000 number of dielectric boundary points 3885 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2526 ## 217 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 10683 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9499005E-09 3.0738470E-09 midg,1,midg; midg,igrid,midg 1.2980331E-08 -1.2435276E-08 1,midg,midg; igrid,midg,midg -2.3604601E-08 3.1162795E-08 gauss-seidel spectral radius is 0.9870934 estimated iterations to convergence 72 setup time was (sec) 0.7300000 now iterating at: 08:57:00 rms-change max change #iterations 0.1647053 21.48411 at 10iterations 1.6646026E-02 2.069115 at 20iterations 1.7424073E-03 0.2118225 at 30iterations 2.3531227E-04 3.1845093E-02 at 40iterations 4.0540992E-05 4.6386719E-03 at 50iterations finished qdiffx linear iterations at : 08:57:04 total time elapsed so far: 5.210000 # loops : 50 mean,max change (kT/e) : 4.0540992E-05 4.6386719E-03 energy calculations done at 5.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.380000 DelPhi exited at 08:57:05 5.387u 0.393s 0:06.10 94.5% 0+0k 0+0io 6pf+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 Wed Feb 15 2012 at 08:57:05 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3338 !!! WARNING: HID 15 has a net charge of 1.4000 !!! WARNING: HID 17 has a net charge of 1.4000 !!! WARNING: ZN5 522 has a net charge of 1.4000 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: 1.896913 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): 32.08200 81.47400 ymin,ymax (A): 25.28900 81.59100 zmin,zma (A): -2.982000 46.36000 x,y,z range (A): 49.39200 56.30199 49.34200 scale (grids/A): 1.896913 object centre (A): 56.77800 53.44000 21.68900 number of atom coordinates read : 3338 total number of charged atoms : 3165 net assigned charge : -0.2999887 assigned positive charge : 507.4063 centred at (gu) : 92.54829 88.84604 93.27746 assigned negative charge : -507.7076 centred at (gu) : 91.88835 89.15649 93.20331 start vw surface at 0.1300000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 93116 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25198 grid for indexing accessible points = 1.400000 m= 36833 mr = 67794 m= 6341 mr = 28768 m= 361 mr = 4305 m= 4 mr = 119 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 1103 time to turn everything in is 0.7700000 number of dielectric boundary points 35669 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 24898 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) : 0.6323044 object centre at (A) : 56.77800 53.44000 21.68900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2302242E-02 -1.7618837E-02 midg,1,midg; midg,igrid,midg 1.3551774E-02 -2.6767673E-02 1,midg,midg; igrid,midg,midg -3.4553364E-02 4.2696059E-02 gauss-seidel spectral radius is 0.9986784 estimated iterations to convergence 218 setup time was (sec) 1.100000 now iterating at: 08:57:06 rms-change max change #iterations 4.933685 183.8103 at 10iterations 2.339962 75.02620 at 20iterations 1.111274 32.71971 at 30iterations 0.5285742 15.38102 at 40iterations 0.2505688 7.734276 at 50iterations 0.1194718 3.319884 at 60iterations 5.6464545E-02 1.560827 at 70iterations 2.6925132E-02 0.8734417 at 80iterations 1.2796023E-02 0.3730659 at 90iterations 6.0723959E-03 0.1766872 at 100iterations 2.8984130E-03 8.2864761E-02 at 110iterations 1.3789847E-03 3.7943125E-02 at 120iterations finished qdiffx linear iterations at : 08:57:25 total time elapsed so far: 19.51000 # loops : 120 mean,max change (kT/e) : 1.3789847E-03 3.7943125E-02 energy calculations done at 19.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.68000 DelPhi exited at 08:57:25 19.683u 0.560s 0:20.53 98.5% 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 Wed Feb 15 2012 at 08:57:25 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3338 !!! WARNING: HID 15 has a net charge of 1.4000 !!! WARNING: HID 17 has a net charge of 1.4000 !!! WARNING: ZN5 522 has a net charge of 1.4000 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: 2.845370 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): 32.08200 81.47400 ymin,ymax (A): 25.28900 81.59100 zmin,zma (A): -2.982000 46.36000 x,y,z range (A): 49.39200 56.30199 49.34200 scale (grids/A): 2.845370 object centre (A): 56.77800 53.44000 21.68900 number of atom coordinates read : 3338 total number of charged atoms : 3165 net assigned charge : -0.2999887 assigned positive charge : 507.4063 centred at (gu) : 93.82223 88.26906 94.91609 assigned negative charge : -507.7076 centred at (gu) : 92.83226 88.73485 94.80489 start vw surface at 0.1500000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 215455 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25198 grid for indexing accessible points = 1.400000 m= 116191 mr = 163358 m= 45982 mr = 98152 m= 11704 mr = 38765 m= 1583 mr = 9196 m= 90 mr = 1062 m= 3 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 1.490000 no. cavity mid-points inaccessible to solvent = 3756 time to turn everything in is 2.510000 number of dielectric boundary points 80442 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 2.770000 number of grid points assigned charge 25320 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) : 1.896913 object centre at (A) : 56.77800 53.44000 21.68900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1485893 -0.1680219 midg,1,midg; midg,igrid,midg 0.2362772 0.1839578 1,midg,midg; igrid,midg,midg -0.3396764 0.4952064 gauss-seidel spectral radius is 0.9992753 estimated iterations to convergence 293 setup time was (sec) 3.150000 now iterating at: 08:57:29 rms-change max change #iterations 11.50569 337.7300 at 10iterations 6.773862 150.5357 at 20iterations 3.956855 73.16970 at 30iterations 2.305334 45.47406 at 40iterations 1.345397 24.39961 at 50iterations 0.7797316 13.42784 at 60iterations 0.4534202 7.325546 at 70iterations 0.2628103 4.129082 at 80iterations 0.1525624 2.565141 at 90iterations 8.8321574E-02 1.499649 at 100iterations 5.1137257E-02 0.8078537 at 110iterations 2.9678648E-02 0.4961329 at 120iterations 1.7258631E-02 0.2773895 at 130iterations 1.0015879E-02 0.1548042 at 140iterations 5.8389045E-03 9.5386505E-02 at 150iterations 3.4281805E-03 6.3078046E-02 at 160iterations 2.0260361E-03 3.3195496E-02 at 170iterations 1.2119045E-03 1.8875122E-02 at 180iterations finished qdiffx linear iterations at : 08:58:02 total time elapsed so far: 35.91000 # loops : 180 mean,max change (kT/e) : 1.2119045E-03 1.8875122E-02 energy calculations done at 35.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 36.08000 DelPhi exited at 08:58:02 36.086u 0.864s 0:37.27 99.1% 0+0k 0+0io 0pf+0w