Tue Oct 11 06:13:33 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 Tue Oct 11 2011 at 06:13:33 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2027 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7480248 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): -17.97200 28.39700 ymin,ymax (A): -11.77700 31.09100 zmin,zma (A): -8.937000 38.65500 x,y,z range (A): 46.36900 42.86800 47.59200 scale (grids/A): 0.7480248 object centre (A): 5.212500 9.657000 14.85900 number of atom coordinates read : 2027 total number of charged atoms : 1908 net assigned charge : 6.931010 assigned positive charge : 309.2101 centred at (gu) : 90.52183 89.98222 90.78601 assigned negative charge : -302.2792 centred at (gu) : 90.37730 89.92008 90.65766 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7937 nv = 96 ne = 84 npr = 40053 no. pairs analyzed = 40053 no. exposed pairs = 2539 no. arc points = 17401 no. surface atoms = 856 nbur = 1171 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 637 mr = 4655 m= 4 mr = 143 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.2400000 number of dielectric boundary points 3780 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1504 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 8224 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8386013E-09 3.3088469E-07 midg,1,midg; midg,igrid,midg 7.2763719E-08 2.1206726E-07 1,midg,midg; igrid,midg,midg -1.9308862E-08 3.3468865E-07 gauss-seidel spectral radius is 0.9906724 estimated iterations to convergence 84 setup time was (sec) 0.4500000 now iterating at: 06:13:33 rms-change max change #iterations 0.2522930 30.10423 at 10iterations 3.5398256E-02 4.277270 at 20iterations 5.1639946E-03 0.6159248 at 30iterations 8.7703305E-04 9.6538544E-02 at 40iterations 2.2058353E-04 2.5154114E-02 at 50iterations finished qdiffx linear iterations at : 06:13:36 total time elapsed so far: 2.830000 # loops : 50 mean,max change (kT/e) : 2.2058353E-04 2.5154114E-02 energy calculations done at 2.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 2.990000 DelPhi exited at 06:13:36 2.998u 0.149s 0:03.54 88.4% 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 Tue Oct 11 2011 at 06:13:36 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2027 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.244075 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): -17.97200 28.39700 ymin,ymax (A): -11.77700 31.09100 zmin,zma (A): -8.937000 38.65500 x,y,z range (A): 46.36900 42.86800 47.59200 scale (grids/A): 2.244075 object centre (A): 5.212500 9.657000 14.85900 number of atom coordinates read : 2027 total number of charged atoms : 1908 net assigned charge : 6.931010 assigned positive charge : 309.2101 centred at (gu) : 91.56570 89.94694 92.35842 assigned negative charge : -302.2792 centred at (gu) : 91.13194 89.76046 91.97311 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 82804 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17401 grid for indexing accessible points = 1.400000 m= 36337 mr = 59143 m= 8539 mr = 28113 m= 1074 mr = 6000 m= 55 mr = 601 m= 0 mr = 9 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 398 time to turn everything in is 0.6200000 number of dielectric boundary points 34943 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 50 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 15210 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) : 0.7480248 object centre at (A) : 5.212500 9.657000 14.85900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0209273E-02 4.9921058E-02 midg,1,midg; midg,igrid,midg 3.2865535E-02 3.0720642E-02 1,midg,midg; igrid,midg,midg 3.5694137E-02 0.1118959 gauss-seidel spectral radius is 0.9989342 estimated iterations to convergence 242 setup time was (sec) 0.8600000 now iterating at: 06:13:37 rms-change max change #iterations 4.982141 191.7830 at 10iterations 2.562765 84.23753 at 20iterations 1.306245 39.07987 at 30iterations 0.6710567 18.10602 at 40iterations 0.3426147 9.371519 at 50iterations 0.1760623 4.935354 at 60iterations 9.0030693E-02 2.788411 at 70iterations 4.6402276E-02 1.301388 at 80iterations 2.3929112E-02 0.7244644 at 90iterations 1.2362609E-02 0.3463135 at 100iterations 6.4442954E-03 0.1822948 at 110iterations 3.4156605E-03 9.1933250E-02 at 120iterations finished qdiffx linear iterations at : 06:13:43 total time elapsed so far: 6.790000 # loops : 120 mean,max change (kT/e) : 3.4156605E-03 9.1933250E-02 energy calculations done at 6.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.960000 DelPhi exited at 06:13:44 6.961u 0.179s 0:07.45 95.7% 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 Tue Oct 11 2011 at 06:13:44 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2027 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.366112 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): -17.97200 28.39700 ymin,ymax (A): -11.77700 31.09100 zmin,zma (A): -8.937000 38.65500 x,y,z range (A): 46.36900 42.86800 47.59200 scale (grids/A): 3.366112 object centre (A): 5.212500 9.657000 14.85900 number of atom coordinates read : 2027 total number of charged atoms : 1908 net assigned charge : 6.931010 assigned positive charge : 309.2101 centred at (gu) : 92.34860 89.92026 93.53760 assigned negative charge : -302.2792 centred at (gu) : 91.69796 89.64063 92.95971 start vw surface at 0.1400000 fill in re-entrant regions at 0.8400000 boundary points on vw surface= 190615 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17401 grid for indexing accessible points = 1.400000 m= 108901 mr = 142110 m= 49955 mr = 91536 m= 16582 mr = 41743 m= 4128 mr = 13197 m= 633 mr = 3096 m= 72 mr = 407 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.9899999 no. cavity mid-points inaccessible to solvent = 1518 time to turn everything in is 1.940000 number of dielectric boundary points 78757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.060000 number of grid points assigned charge 15264 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) : 2.244075 object centre at (A) : 5.212500 9.657000 14.85900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6047854 0.4911965 midg,1,midg; midg,igrid,midg 0.2580529 0.1296517 1,midg,midg; igrid,midg,midg 0.2381182 0.7750389 gauss-seidel spectral radius is 0.9993243 estimated iterations to convergence 303 setup time was (sec) 2.220000 now iterating at: 06:13:46 rms-change max change #iterations 10.87766 387.0704 at 10iterations 6.567545 157.7297 at 20iterations 3.945876 89.29504 at 30iterations 2.360000 42.81487 at 40iterations 1.410299 25.94797 at 50iterations 0.8397674 15.93924 at 60iterations 0.4997086 9.637020 at 70iterations 0.2973267 5.456213 at 80iterations 0.1768534 3.290466 at 90iterations 0.1051351 1.977102 at 100iterations 6.2568188E-02 1.083012 at 110iterations 3.7457440E-02 0.6619263 at 120iterations 2.2635361E-02 0.3818321 at 130iterations 1.3897634E-02 0.2217941 at 140iterations 8.8113099E-03 0.1471481 at 150iterations 5.8389897E-03 0.1115189 at 160iterations 4.0982547E-03 7.2513580E-02 at 170iterations 3.0525518E-03 6.0153961E-02 at 180iterations finished qdiffx linear iterations at : 06:13:56 total time elapsed so far: 11.93000 # loops : 180 mean,max change (kT/e) : 3.0525518E-03 6.0153961E-02 energy calculations done at 11.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.12000 DelPhi exited at 06:13:57 12.118u 0.172s 0:12.71 96.6% 0+0k 0+0io 0pf+0w