Mon Oct 10 17:04:25 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 Mon Oct 10 2011 at 17:04:26 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 = 2983 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: 0.5647566 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): -30.50300 32.53300 ymin,ymax (A): -20.61000 26.35100 zmin,zma (A): -7.363000 40.68400 x,y,z range (A): 63.03600 46.96100 48.04700 scale (grids/A): 0.5647566 object centre (A): 1.015000 2.870500 16.66050 number of atom coordinates read : 2983 total number of charged atoms : 2843 net assigned charge : 0.5000191 assigned positive charge : 447.0329 centred at (gu) : 90.75354 90.31070 89.58855 assigned negative charge : -446.5341 centred at (gu) : 90.75519 90.14152 89.48005 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6210 nv = 96 ne = 84 npr = 60398 no. pairs analyzed = 60398 no. exposed pairs = 3791 no. arc points = 26887 no. surface atoms = 1276 nbur = 1707 mkacc time = 0.1500000 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 = 1.512000 m= 237 mr = 3183 m= 0 mr = 7 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3200000 number of dielectric boundary points 3257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2762 ## 307 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8059 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5286012E-09 1.3339925E-09 midg,1,midg; midg,igrid,midg -2.0463928E-09 2.4233242E-09 1,midg,midg; igrid,midg,midg 7.2824760E-11 5.1696893E-11 gauss-seidel spectral radius is 0.9838268 estimated iterations to convergence 65 setup time was (sec) 0.6200000 now iterating at: 17:04:27 rms-change max change #iterations 8.2937904E-02 13.81426 at 10iterations 6.0563409E-03 1.055752 at 20iterations 4.4471800E-04 6.9007397E-02 at 30iterations 3.4347540E-05 5.1383972E-03 at 40iterations 3.0956394E-06 5.9318542E-04 at 50iterations finished qdiffx linear iterations at : 17:04:31 total time elapsed so far: 4.330000 # loops : 50 mean,max change (kT/e) : 3.0956394E-06 5.9318542E-04 energy calculations done at 4.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.510000 DelPhi exited at 17:04:33 4.517u 0.382s 0:06.52 75.0% 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 Mon Oct 10 2011 at 17:04:33 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 = 2983 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: 1.694270 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): -30.50300 32.53300 ymin,ymax (A): -20.61000 26.35100 zmin,zma (A): -7.363000 40.68400 x,y,z range (A): 63.03600 46.96100 48.04700 scale (grids/A): 1.694270 object centre (A): 1.015000 2.870500 16.66050 number of atom coordinates read : 2983 total number of charged atoms : 2843 net assigned charge : 0.5000191 assigned positive charge : 447.0329 centred at (gu) : 92.26006 90.93115 88.76511 assigned negative charge : -446.5341 centred at (gu) : 92.26527 90.42434 88.43983 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 68759 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26887 grid for indexing accessible points = 1.400000 m= 20836 mr = 46562 m= 2177 mr = 14154 m= 61 mr = 1067 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1058 time to turn everything in is 0.5400000 number of dielectric boundary points 30035 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 314 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 21991 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) : 0.5647566 object centre at (A) : 1.015000 2.870500 16.66050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9645002E-03 4.0014330E-03 midg,1,midg; midg,igrid,midg -1.8939424E-02 1.4473479E-02 1,midg,midg; igrid,midg,midg 3.9706109E-03 1.8254098E-02 gauss-seidel spectral radius is 0.9983183 estimated iterations to convergence 194 setup time was (sec) 0.8400000 now iterating at: 17:04:34 rms-change max change #iterations 3.611143 160.5656 at 10iterations 1.553867 56.07462 at 20iterations 0.6665801 27.01025 at 30iterations 0.2879704 9.954329 at 40iterations 0.1237996 4.616884 at 50iterations 5.3462233E-02 1.874076 at 60iterations 2.2948425E-02 0.8227730 at 70iterations 9.9038258E-03 0.3544922 at 80iterations 4.2589884E-03 0.1526947 at 90iterations 1.8439039E-03 5.9958458E-02 at 100iterations 7.9127226E-04 2.8388977E-02 at 110iterations 3.4127722E-04 1.2104988E-02 at 120iterations finished qdiffx linear iterations at : 17:04:43 total time elapsed so far: 10.15000 # loops : 120 mean,max change (kT/e) : 3.4127722E-04 1.2104988E-02 energy calculations done at 10.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.32000 DelPhi exited at 17:04:44 10.327u 0.454s 0:11.84 90.9% 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 17:04:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2983 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: 2.541405 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): -30.50300 32.53300 ymin,ymax (A): -20.61000 26.35100 zmin,zma (A): -7.363000 40.68400 x,y,z range (A): 63.03600 46.96100 48.04700 scale (grids/A): 2.541405 object centre (A): 1.015000 2.870500 16.66050 number of atom coordinates read : 2983 total number of charged atoms : 2843 net assigned charge : 0.5000191 assigned positive charge : 447.0329 centred at (gu) : 93.38982 91.39659 88.14759 assigned negative charge : -446.5341 centred at (gu) : 93.39770 90.63641 87.65951 start vw surface at 0.1300000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 159623 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26887 grid for indexing accessible points = 1.400000 m= 72190 mr = 113657 m= 20310 mr = 57183 m= 3358 mr = 14961 m= 270 mr = 2200 m= 3 mr = 151 m= 0 mr = 0 time to grow re-entrant surface = 0.8100001 no. cavity mid-points inaccessible to solvent = 3388 time to turn everything in is 1.350000 number of dielectric boundary points 67602 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 22728 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) : 1.694270 object centre at (A) : 1.015000 2.870500 16.66050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7654107E-02 5.2948613E-02 midg,1,midg; midg,igrid,midg -0.2270545 0.2151822 1,midg,midg; igrid,midg,midg 0.2088938 0.3455878 gauss-seidel spectral radius is 0.9991825 estimated iterations to convergence 276 setup time was (sec) 1.660000 now iterating at: 17:04:47 rms-change max change #iterations 9.145181 299.9456 at 10iterations 5.195945 118.8999 at 20iterations 2.935383 76.64242 at 30iterations 1.656260 35.68100 at 40iterations 0.9307771 22.82088 at 50iterations 0.5214250 11.14449 at 60iterations 0.2929164 6.104675 at 70iterations 0.1636218 3.501926 at 80iterations 9.1599278E-02 1.855011 at 90iterations 5.1264983E-02 1.013421 at 100iterations 2.8595455E-02 0.5833130 at 110iterations 1.5962603E-02 0.3157930 at 120iterations 8.9067882E-03 0.1695518 at 130iterations 4.9741082E-03 9.9159241E-02 at 140iterations 2.7752069E-03 5.5656433E-02 at 150iterations 1.5470885E-03 3.0879974E-02 at 160iterations 8.6387020E-04 1.6887188E-02 at 170iterations 4.8206685E-04 9.3212128E-03 at 180iterations finished qdiffx linear iterations at : 17:05:02 total time elapsed so far: 17.10000 # loops : 180 mean,max change (kT/e) : 4.8206685E-04 9.3212128E-03 energy calculations done at 17.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.27000 DelPhi exited at 17:05:03 17.272u 0.460s 0:18.50 95.8% 0+0k 0+0io 0pf+0w