Tue Oct 11 08:09:39 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 08:09:39 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1326 !!! WARNING: GLM 168 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7060970 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): -39.93300 7.922000 ymin,ymax (A): -61.62600 -11.20800 zmin,zma (A): -33.63600 9.102000 x,y,z range (A): 47.85500 50.41800 42.73800 scale (grids/A): 0.7060970 object centre (A): -16.00550 -36.41700 -12.26700 number of atom coordinates read : 1326 total number of charged atoms : 1189 net assigned charge : -0.5939953 assigned positive charge : 192.0432 centred at (gu) : 88.28048 90.12412 88.59987 assigned negative charge : -192.6371 centred at (gu) : 88.30203 90.06281 88.71176 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 4617 nv = 96 ne = 84 npr = 25230 no. pairs analyzed = 25230 no. exposed pairs = 2063 no. arc points = 15186 no. surface atoms = 679 nbur = 647 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 304 mr = 2024 m= 0 mr = 21 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2876 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1230 ## 115 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 4842 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.6137781E-08 -2.9480699E-08 midg,1,midg; midg,igrid,midg -2.3093151E-08 1.2827479E-08 1,midg,midg; igrid,midg,midg 1.3779881E-09 -8.4936600E-09 gauss-seidel spectral radius is 0.9894890 estimated iterations to convergence 79 setup time was (sec) 0.5000000 now iterating at: 08:09:40 rms-change max change #iterations 0.1566786 30.70270 at 10iterations 1.8592285E-02 3.686862 at 20iterations 2.2198162E-03 0.4574132 at 30iterations 2.6353402E-04 4.7660828E-02 at 40iterations 3.1284126E-05 5.3997040E-03 at 50iterations finished qdiffx linear iterations at : 08:09:43 total time elapsed so far: 3.870000 # loops : 50 mean,max change (kT/e) : 3.1284126E-05 5.3997040E-03 energy calculations done at 3.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.040000 DelPhi exited at 08:09:44 4.046u 0.252s 0:04.76 90.1% 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 08:09:44 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1326 !!! WARNING: GLM 168 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.118291 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): -39.93300 7.922000 ymin,ymax (A): -61.62600 -11.20800 zmin,zma (A): -33.63600 9.102000 x,y,z range (A): 47.85500 50.41800 42.73800 scale (grids/A): 2.118291 object centre (A): -16.00550 -36.41700 -12.26700 number of atom coordinates read : 1326 total number of charged atoms : 1189 net assigned charge : -0.5939953 assigned positive charge : 192.0432 centred at (gu) : 84.84151 90.37257 85.79964 assigned negative charge : -192.6371 centred at (gu) : 84.90635 90.18839 86.13529 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 47493 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15186 grid for indexing accessible points = 1.400000 m= 16371 mr = 28116 m= 3155 mr = 10949 m= 276 mr = 1792 m= 16 mr = 83 m= 0 mr = 3 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 26368 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 9451 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) : 0.7060970 object centre at (A) : -16.00550 -36.41700 -12.26700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3303740E-03 -1.3112094E-02 midg,1,midg; midg,igrid,midg -1.8754372E-02 -1.1467793E-03 1,midg,midg; igrid,midg,midg -1.6011335E-02 3.4575462E-03 gauss-seidel spectral radius is 0.9987664 estimated iterations to convergence 225 setup time was (sec) 0.7700000 now iterating at: 08:09:45 rms-change max change #iterations 3.580926 189.8284 at 10iterations 1.728406 69.69401 at 20iterations 0.8353871 33.52256 at 30iterations 0.4036739 15.57053 at 40iterations 0.1955095 8.025291 at 50iterations 9.3933709E-02 3.331028 at 60iterations 4.5511469E-02 1.753098 at 70iterations 2.1980718E-02 0.8660355 at 80iterations 1.0598396E-02 0.4051461 at 90iterations 5.1320484E-03 0.1918335 at 100iterations 2.4794436E-03 0.1010017 at 110iterations 1.2022924E-03 5.0411105E-02 at 120iterations finished qdiffx linear iterations at : 08:09:53 total time elapsed so far: 8.980000 # loops : 120 mean,max change (kT/e) : 1.2022924E-03 5.0411105E-02 energy calculations done at 8.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.160000 DelPhi exited at 08:09:54 9.163u 0.331s 0:09.96 95.2% 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 08:09:54 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1326 !!! WARNING: GLM 168 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.177436 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): -39.93300 7.922000 ymin,ymax (A): -61.62600 -11.20800 zmin,zma (A): -33.63600 9.102000 x,y,z range (A): 47.85500 50.41800 42.73800 scale (grids/A): 3.177436 object centre (A): -16.00550 -36.41700 -12.26700 number of atom coordinates read : 1326 total number of charged atoms : 1189 net assigned charge : -0.5939953 assigned positive charge : 192.0432 centred at (gu) : 82.26228 90.55892 83.69955 assigned negative charge : -192.6371 centred at (gu) : 82.35948 90.28262 84.20300 start vw surface at 0.1200000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 109184 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15186 grid for indexing accessible points = 1.400000 m= 50502 mr = 68873 m= 19945 mr = 38393 m= 5700 mr = 15121 m= 1015 mr = 3923 m= 128 mr = 582 m= 13 mr = 71 m= 0 mr = 5 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.430000 number of dielectric boundary points 59519 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 9512 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) : 2.118291 object centre at (A) : -16.00550 -36.41700 -12.26700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0466692E-02 -8.7315492E-02 midg,1,midg; midg,igrid,midg -0.1000623 -8.9986930E-03 1,midg,midg; igrid,midg,midg -0.2379382 5.0757356E-02 gauss-seidel spectral radius is 0.9992888 estimated iterations to convergence 296 setup time was (sec) 1.740000 now iterating at: 08:09:56 rms-change max change #iterations 8.270202 343.7119 at 10iterations 4.910598 140.1936 at 20iterations 2.891066 74.17007 at 30iterations 1.689492 39.90398 at 40iterations 0.9851589 21.14292 at 50iterations 0.5747262 14.68703 at 60iterations 0.3342747 7.867429 at 70iterations 0.1934774 4.383167 at 80iterations 0.1124919 2.249226 at 90iterations 6.5144874E-02 1.610017 at 100iterations 3.7794486E-02 0.7751923 at 110iterations 2.1876164E-02 0.5477152 at 120iterations 1.2682410E-02 0.2619311 at 130iterations 7.3324428E-03 0.1576905 at 140iterations 4.2609237E-03 9.2895508E-02 at 150iterations 2.4708349E-03 5.2520752E-02 at 160iterations 1.4296075E-03 2.9697418E-02 at 170iterations 8.2708307E-04 1.7526627E-02 at 180iterations finished qdiffx linear iterations at : 08:10:10 total time elapsed so far: 15.30000 # loops : 180 mean,max change (kT/e) : 8.2708307E-04 1.7526627E-02 energy calculations done at 15.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.49000 DelPhi exited at 08:10:10 15.491u 0.320s 0:16.44 96.1% 0+0k 0+0io 0pf+0w