Sun Oct 9 14:36:28 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 Sun Oct 9 2011 at 14:36:28 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 = 2707 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5678918 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): -0.3370000 51.82000 ymin,ymax (A): -10.04600 39.97400 zmin,zma (A): -15.80000 46.88800 x,y,z range (A): 52.15700 50.02000 62.68800 scale (grids/A): 0.5678918 object centre (A): 25.74150 14.96400 15.54400 number of atom coordinates read : 2707 total number of charged atoms : 2565 net assigned charge : 6.539022 assigned positive charge : 412.3195 centred at (gu) : 89.72753 90.50024 88.53742 assigned negative charge : -405.7815 centred at (gu) : 89.69113 90.39674 88.57787 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5695 nv = 96 ne = 84 npr = 53474 no. pairs analyzed = 53474 no. exposed pairs = 3526 no. arc points = 25198 no. surface atoms = 1192 nbur = 1515 mkacc time = 9.0000004E-02 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= 239 mr = 2829 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3098 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2619 ## 342 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7369 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0508060E-09 2.7267408E-10 midg,1,midg; midg,igrid,midg -4.2214410E-10 2.5620031E-09 1,midg,midg; igrid,midg,midg 4.5242010E-10 1.3088863E-09 gauss-seidel spectral radius is 0.9839815 estimated iterations to convergence 65 setup time was (sec) 0.3900000 now iterating at: 14:36:28 rms-change max change #iterations 8.3987691E-02 14.46592 at 10iterations 6.2743081E-03 0.9346962 at 20iterations 4.9001211E-04 7.6309204E-02 at 30iterations 5.1027590E-05 8.1043243E-03 at 40iterations 9.1097299E-06 1.2817383E-03 at 50iterations finished qdiffx linear iterations at : 14:36:31 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 9.1097299E-06 1.2817383E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 14:36:32 3.443u 0.198s 0:03.95 91.8% 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 Sun Oct 9 2011 at 14:36:32 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 = 2707 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.703676 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): -0.3370000 51.82000 ymin,ymax (A): -10.04600 39.97400 zmin,zma (A): -15.80000 46.88800 x,y,z range (A): 52.15700 50.02000 62.68800 scale (grids/A): 1.703676 object centre (A): 25.74150 14.96400 15.54400 number of atom coordinates read : 2707 total number of charged atoms : 2565 net assigned charge : 6.539022 assigned positive charge : 412.3195 centred at (gu) : 89.18206 91.49993 85.61149 assigned negative charge : -405.7815 centred at (gu) : 89.07321 91.18992 85.73349 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 62235 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25198 grid for indexing accessible points = 1.400000 m= 19346 mr = 41115 m= 2160 mr = 13080 m= 69 mr = 966 m= 0 mr = 4 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 28645 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 299 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 19801 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) : 0.5678918 object centre at (A) : 25.74150 14.96400 15.54400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6795953E-02 1.1738015E-02 midg,1,midg; midg,igrid,midg -1.7722999E-03 4.0535592E-03 1,midg,midg; igrid,midg,midg -1.0832865E-02 -1.4834728E-03 gauss-seidel spectral radius is 0.9983171 estimated iterations to convergence 194 setup time was (sec) 0.5700000 now iterating at: 14:36:32 rms-change max change #iterations 3.439921 150.8734 at 10iterations 1.474949 52.14135 at 20iterations 0.6374916 23.01898 at 30iterations 0.2738848 9.336609 at 40iterations 0.1182614 4.494667 at 50iterations 5.0887886E-02 1.676617 at 60iterations 2.1862362E-02 0.8064213 at 70iterations 9.4435597E-03 0.3769836 at 80iterations 4.0762569E-03 0.1867599 at 90iterations 1.7579051E-03 6.5832615E-02 at 100iterations 7.6471380E-04 2.6172638E-02 at 110iterations 3.2981369E-04 1.3042450E-02 at 120iterations finished qdiffx linear iterations at : 14:36:40 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 3.2981369E-04 1.3042450E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 14:36:40 7.884u 0.196s 0:08.41 95.9% 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 Sun Oct 9 2011 at 14:36:40 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 = 2707 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.555513 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): -0.3370000 51.82000 ymin,ymax (A): -10.04600 39.97400 zmin,zma (A): -15.80000 46.88800 x,y,z range (A): 52.15700 50.02000 62.68800 scale (grids/A): 2.555513 object centre (A): 25.74150 14.96400 15.54400 number of atom coordinates read : 2707 total number of charged atoms : 2565 net assigned charge : 6.539022 assigned positive charge : 412.3195 centred at (gu) : 88.77292 92.24963 83.41694 assigned negative charge : -405.7815 centred at (gu) : 88.60966 91.78479 83.60015 start vw surface at 0.1000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 144480 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25198 grid for indexing accessible points = 1.400000 m= 66180 mr = 101003 m= 19474 mr = 51476 m= 3270 mr = 14432 m= 274 mr = 1971 m= 8 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7800000 number of dielectric boundary points 64679 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 20494 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) : 1.703676 object centre at (A) : 25.74150 14.96400 15.54400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.034017 0.1610855 midg,1,midg; midg,igrid,midg -3.9332826E-02 1.8165527E-02 1,midg,midg; igrid,midg,midg -0.1280700 -4.6779331E-02 gauss-seidel spectral radius is 0.9991744 estimated iterations to convergence 275 setup time was (sec) 1.020000 now iterating at: 14:36:41 rms-change max change #iterations 8.841364 275.9437 at 10iterations 5.091257 135.5228 at 20iterations 2.901527 67.89314 at 30iterations 1.643690 38.14927 at 40iterations 0.9300390 21.80604 at 50iterations 0.5226566 10.89639 at 60iterations 0.2948005 6.662296 at 70iterations 0.1654536 3.403019 at 80iterations 9.2556387E-02 2.436295 at 90iterations 5.1808577E-02 1.146060 at 100iterations 2.8957389E-02 0.6403711 at 110iterations 1.6171513E-02 0.3647671 at 120iterations 9.0389401E-03 0.1942854 at 130iterations 5.0480152E-03 0.1114225 at 140iterations 2.8200631E-03 5.9221268E-02 at 150iterations 1.5766637E-03 3.2882690E-02 at 160iterations 8.8563008E-04 1.7680645E-02 at 170iterations 4.9795560E-04 1.0675430E-02 at 180iterations finished qdiffx linear iterations at : 14:36:53 total time elapsed so far: 12.37000 # loops : 180 mean,max change (kT/e) : 4.9795560E-04 1.0675430E-02 energy calculations done at 12.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.51000 DelPhi exited at 14:36:53 12.514u 0.214s 0:13.03 97.6% 0+0k 0+0io 0pf+0w