Sun Oct 9 12:43:46 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 12:43:46 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2922 !!! WARNING: GLM 273 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6221818 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): -20.55700 28.95900 ymin,ymax (A): -22.13500 35.08300 zmin,zma (A): -15.70200 37.09200 x,y,z range (A): 49.51600 57.21800 52.79400 scale (grids/A): 0.6221818 object centre (A): 4.201000 6.474000 10.69500 number of atom coordinates read : 2922 total number of charged atoms : 2770 net assigned charge : 5.906020 assigned positive charge : 462.2490 centred at (gu) : 89.73765 90.01062 91.01842 assigned negative charge : -456.3439 centred at (gu) : 89.80695 90.13528 90.95515 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7346 nv = 96 ne = 84 npr = 57575 no. pairs analyzed = 57575 no. exposed pairs = 3756 no. arc points = 25603 no. surface atoms = 1258 nbur = 1664 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 367 mr = 3870 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.2100000 number of dielectric boundary points 3819 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2648 ## 307 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9114 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8243208E-10 1.2803240E-08 midg,1,midg; midg,igrid,midg 1.5207535E-08 -5.5225011E-09 1,midg,midg; igrid,midg,midg 1.1368694E-08 -7.3988354E-10 gauss-seidel spectral radius is 0.9866441 estimated iterations to convergence 71 setup time was (sec) 0.4000000 now iterating at: 12:43:47 rms-change max change #iterations 0.1411387 18.67890 at 10iterations 1.3377110E-02 1.687132 at 20iterations 1.4922550E-03 0.2134705 at 30iterations 2.4131425E-04 4.5261383E-02 at 40iterations 5.2827589E-05 1.0490417E-02 at 50iterations finished qdiffx linear iterations at : 12:43:49 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 5.2827589E-05 1.0490417E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 12:43:50 3.411u 0.180s 0:03.87 92.7% 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 Sun Oct 9 2011 at 12:43:50 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2922 !!! WARNING: GLM 273 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.866545 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): -20.55700 28.95900 ymin,ymax (A): -22.13500 35.08300 zmin,zma (A): -15.70200 37.09200 x,y,z range (A): 49.51600 57.21800 52.79400 scale (grids/A): 1.866545 object centre (A): 4.201000 6.474000 10.69500 number of atom coordinates read : 2922 total number of charged atoms : 2770 net assigned charge : 5.906020 assigned positive charge : 462.2490 centred at (gu) : 89.21205 90.03103 93.05473 assigned negative charge : -456.3439 centred at (gu) : 89.42036 90.40556 92.86519 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79346 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25603 grid for indexing accessible points = 1.400000 m= 27486 mr = 54268 m= 3650 mr = 19362 m= 220 mr = 1901 m= 4 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 316 time to turn everything in is 0.3900000 number of dielectric boundary points 35112 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 247 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 21744 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) : 0.6221818 object centre at (A) : 4.201000 6.474000 10.69500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8186375E-03 4.1041642E-02 midg,1,midg; midg,igrid,midg 3.8815696E-02 -4.2385422E-02 1,midg,midg; igrid,midg,midg 2.1247754E-02 1.2249872E-02 gauss-seidel spectral radius is 0.9986098 estimated iterations to convergence 213 setup time was (sec) 0.6200000 now iterating at: 12:43:51 rms-change max change #iterations 4.501011 167.0783 at 10iterations 2.091625 66.03939 at 20iterations 0.9712645 31.57933 at 30iterations 0.4531041 16.60328 at 40iterations 0.2108637 6.613403 at 50iterations 9.7917750E-02 3.157372 at 60iterations 4.5720033E-02 1.421965 at 70iterations 2.1407524E-02 0.6780415 at 80iterations 1.0037778E-02 0.3186569 at 90iterations 4.7483025E-03 0.1612854 at 100iterations 2.2836020E-03 8.0184937E-02 at 110iterations 1.1206308E-03 3.9995193E-02 at 120iterations finished qdiffx linear iterations at : 12:43:58 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 1.1206308E-03 3.9995193E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 12:43:58 7.902u 0.190s 0:08.42 96.0% 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 Sun Oct 9 2011 at 12:43:58 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2922 !!! WARNING: GLM 273 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.799818 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): -20.55700 28.95900 ymin,ymax (A): -22.13500 35.08300 zmin,zma (A): -15.70200 37.09200 x,y,z range (A): 49.51600 57.21800 52.79400 scale (grids/A): 2.799818 object centre (A): 4.201000 6.474000 10.69500 number of atom coordinates read : 2922 total number of charged atoms : 2770 net assigned charge : 5.906020 assigned positive charge : 462.2490 centred at (gu) : 88.81797 90.04639 94.58187 assigned negative charge : -456.3439 centred at (gu) : 89.13053 90.60813 94.29771 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 183439 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25603 grid for indexing accessible points = 1.400000 m= 90866 mr = 132164 m= 30215 mr = 72540 m= 6162 mr = 23076 m= 874 mr = 4103 m= 31 mr = 490 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 1156 time to turn everything in is 1.010000 number of dielectric boundary points 79209 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 22160 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) : 1.866545 object centre at (A) : 4.201000 6.474000 10.69500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4005661E-02 0.6536214 midg,1,midg; midg,igrid,midg 0.4328424 -0.4157378 1,midg,midg; igrid,midg,midg 0.1939027 4.9742427E-02 gauss-seidel spectral radius is 0.9992617 estimated iterations to convergence 290 setup time was (sec) 1.240000 now iterating at: 12:44:00 rms-change max change #iterations 10.93557 363.6489 at 10iterations 6.557181 157.6972 at 20iterations 3.894470 85.48944 at 30iterations 2.298139 47.60558 at 40iterations 1.352420 29.99889 at 50iterations 0.7914162 16.49126 at 60iterations 0.4625745 9.598900 at 70iterations 0.2690408 5.539021 at 80iterations 0.1562902 3.303499 at 90iterations 9.0684399E-02 1.681442 at 100iterations 5.2781891E-02 0.9968109 at 110iterations 3.0654473E-02 0.5667934 at 120iterations 1.7863406E-02 0.3247833 at 130iterations 1.0452937E-02 0.2002831 at 140iterations 6.1823130E-03 0.1297684 at 150iterations 3.7175016E-03 7.0991516E-02 at 160iterations 2.2861897E-03 4.8194885E-02 at 170iterations 1.4578566E-03 3.4072876E-02 at 180iterations finished qdiffx linear iterations at : 12:44:11 total time elapsed so far: 12.73000 # loops : 180 mean,max change (kT/e) : 1.4578566E-03 3.4072876E-02 energy calculations done at 12.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.86000 DelPhi exited at 12:44:12 12.865u 0.225s 0:13.43 97.3% 0+0k 0+0io 0pf+0w