Mon Oct 10 14:38:30 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 Mon Oct 10 2011 at 14:38:30 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3709 !!! WARNING: GLN 328 has a net charge of -0.2720 !!! WARNING: ADP 1298 has a net charge of -2.0000 !!! WARNING: MG1 1299 has a net charge of 1.4000 !!! WARNING: MG1 1302 has a net charge of 1.4000 !!! WARNING: MG1 1303 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.3440578 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): -12.69500 57.02800 ymin,ymax (A): 2.270000 65.40700 zmin,zma (A): -4.964000 98.50700 x,y,z range (A): 69.72300 63.13700 103.4710 scale (grids/A): 0.3440578 object centre (A): 22.16650 33.83850 46.77150 number of atom coordinates read : 3709 total number of charged atoms : 3475 net assigned charge : -2.571983 assigned positive charge : 578.3190 centred at (gu) : 87.61336 89.73696 84.50040 assigned negative charge : -580.8928 centred at (gu) : 87.60255 89.77284 84.45172 start vw surface at 0.2200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 2536 nv = 96 ne = 84 npr = 68918 no. pairs analyzed = 68918 no. exposed pairs = 5623 no. arc points = 39931 no. surface atoms = 1866 nbur = 1843 mkacc time = 0.2100000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.436000 m= 48 mr = 895 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 1689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2399 ## 780 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 3613 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5881237E-14 2.5282859E-16 midg,1,midg; midg,igrid,midg 1.5150157E-15 -2.0531412E-15 1,midg,midg; igrid,midg,midg -2.4663435E-15 3.6857907E-17 gauss-seidel spectral radius is 0.9573396 estimated iterations to convergence 41 setup time was (sec) 0.7400000 now iterating at: 14:38:31 rms-change max change #iterations 6.4767688E-03 1.959026 at 10iterations 2.6905193E-04 9.3811035E-02 at 20iterations 2.8406132E-05 9.4051361E-03 at 30iterations 3.2451687E-06 1.0604858E-03 at 40iterations 3.7108083E-07 1.2207031E-04 at 50iterations finished qdiffx linear iterations at : 14:38:35 total time elapsed so far: 4.290000 # loops : 50 mean,max change (kT/e) : 3.7108083E-07 1.2207031E-04 energy calculations done at 4.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.540000 DelPhi exited at 14:38:36 4.547u 0.195s 0:05.28 89.5% 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 Mon Oct 10 2011 at 14:38:36 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3709 !!! WARNING: GLN 328 has a net charge of -0.2720 !!! WARNING: ADP 1298 has a net charge of -2.0000 !!! WARNING: MG1 1299 has a net charge of 1.4000 !!! WARNING: MG1 1302 has a net charge of 1.4000 !!! WARNING: MG1 1303 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.032173 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): -12.69500 57.02800 ymin,ymax (A): 2.270000 65.40700 zmin,zma (A): -4.964000 98.50700 x,y,z range (A): 69.72300 63.13700 103.4710 scale (grids/A): 1.032173 object centre (A): 22.16650 33.83850 46.77150 number of atom coordinates read : 3709 total number of charged atoms : 3475 net assigned charge : -2.571983 assigned positive charge : 578.3190 centred at (gu) : 82.83924 89.21033 73.49993 assigned negative charge : -580.8928 centred at (gu) : 82.80747 89.31815 73.35449 start vw surface at 0.2100000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 30570 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39931 initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.358720 m= 4619 mr = 17027 m= 128 mr = 1873 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 39 time to turn everything in is 0.4400000 number of dielectric boundary points 16417 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1244 ## 88 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 20956 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) : 0.3440578 object centre at (A) : 22.16650 33.83850 46.77150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.8014127E-04 2.4809517E-05 midg,1,midg; midg,igrid,midg -1.1327489E-04 -2.6228564E-04 1,midg,midg; igrid,midg,midg -1.6036401E-04 2.9342629E-05 gauss-seidel spectral radius is 0.9952911 estimated iterations to convergence 117 setup time was (sec) 0.8000000 now iterating at: 14:38:37 rms-change max change #iterations 1.138976 95.31868 at 10iterations 0.2763260 19.00309 at 20iterations 6.7571729E-02 4.502247 at 30iterations 1.6672732E-02 1.014772 at 40iterations 4.1879988E-03 0.2541752 at 50iterations 1.1862970E-03 8.5376740E-02 at 60iterations 4.1944353E-04 3.0008316E-02 at 70iterations 1.9294200E-04 1.3715744E-02 at 80iterations 9.9839111E-05 6.7873001E-03 at 90iterations 5.3249645E-05 3.7040710E-03 at 100iterations 2.8657027E-05 2.0179749E-03 at 110iterations 1.5455849E-05 1.1024475E-03 at 120iterations finished qdiffx linear iterations at : 14:38:45 total time elapsed so far: 8.800000 # loops : 120 mean,max change (kT/e) : 1.5455849E-05 1.1024475E-03 energy calculations done at 8.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.030000 DelPhi exited at 14:38:45 9.034u 0.232s 0:09.54 97.0% 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 Mon Oct 10 2011 at 14:38:45 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3709 !!! WARNING: GLN 328 has a net charge of -0.2720 !!! WARNING: ADP 1298 has a net charge of -2.0000 !!! WARNING: MG1 1299 has a net charge of 1.4000 !!! WARNING: MG1 1302 has a net charge of 1.4000 !!! WARNING: MG1 1303 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.548260 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): -12.69500 57.02800 ymin,ymax (A): 2.270000 65.40700 zmin,zma (A): -4.964000 98.50700 x,y,z range (A): 69.72300 63.13700 103.4710 scale (grids/A): 1.548260 object centre (A): 22.16650 33.83850 46.77150 number of atom coordinates read : 3709 total number of charged atoms : 3475 net assigned charge : -2.571983 assigned positive charge : 578.3190 centred at (gu) : 79.25855 88.81532 65.24966 assigned negative charge : -580.8928 centred at (gu) : 79.21122 88.97710 65.03167 start vw surface at 0.2200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 72539 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39931 initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.329600 m= 20260 mr = 44549 m= 1834 mr = 12181 m= 35 mr = 764 m= 0 mr = 2 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 138 time to turn everything in is 0.8700000 number of dielectric boundary points 37172 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 576 ## 13 charges are in solution ## iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 26196 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) : 1.032173 object centre at (A) : 22.16650 33.83850 46.77150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0304998E-02 1.0075592E-03 midg,1,midg; midg,igrid,midg -6.4776717E-03 -1.6386239E-02 1,midg,midg; igrid,midg,midg -7.9984525E-03 1.6872749E-03 gauss-seidel spectral radius is 0.9979873 estimated iterations to convergence 177 setup time was (sec) 1.250000 now iterating at: 14:38:47 rms-change max change #iterations 4.174033 201.4590 at 10iterations 1.721875 73.82977 at 20iterations 0.7039586 35.67228 at 30iterations 0.2875363 11.26134 at 40iterations 0.1160494 4.427399 at 50iterations 4.6724387E-02 1.966257 at 60iterations 1.8858608E-02 0.7489891 at 70iterations 7.6006325E-03 0.2617188 at 80iterations 3.0945581E-03 0.1223927 at 90iterations 1.2818816E-03 5.2696228E-02 at 100iterations 5.6503905E-04 2.2447586E-02 at 110iterations 2.7628732E-04 1.2615204E-02 at 120iterations 1.5447891E-04 6.9131851E-03 at 130iterations 9.6040079E-05 4.3802261E-03 at 140iterations 6.3147898E-05 2.8667450E-03 at 150iterations 4.2443960E-05 1.9321442E-03 at 160iterations 2.8756645E-05 1.3113022E-03 at 170iterations 1.9536745E-05 8.9645386E-04 at 180iterations finished qdiffx linear iterations at : 14:38:59 total time elapsed so far: 13.74000 # loops : 180 mean,max change (kT/e) : 1.9536745E-05 8.9645386E-04 energy calculations done at 13.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.99000 DelPhi exited at 14:39:00 13.990u 0.228s 0:14.77 96.2% 0+0k 0+0io 0pf+0w