Tue Oct 11 07:51:16 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 Tue Oct 11 2011 at 07:51:16 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 = 2374 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: 0.6418115 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): -9.044000 36.56100 ymin,ymax (A): -14.63700 40.83100 zmin,zma (A): 5.167000 52.62900 x,y,z range (A): 45.60500 55.46800 47.46200 scale (grids/A): 0.6418115 object centre (A): 13.75850 13.09700 28.89800 number of atom coordinates read : 2374 total number of charged atoms : 2238 net assigned charge : 4.500007 assigned positive charge : 356.5233 centred at (gu) : 90.50074 88.72300 90.69559 assigned negative charge : -352.0238 centred at (gu) : 90.41270 88.72941 90.84122 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6476 nv = 96 ne = 84 npr = 48211 no. pairs analyzed = 48211 no. exposed pairs = 2853 no. arc points = 19885 no. surface atoms = 980 nbur = 1394 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 357 mr = 3602 m= 2 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3176 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2070 ## 205 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7863 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9708715E-08 -1.1064972E-08 midg,1,midg; midg,igrid,midg 1.0017487E-08 4.8229967E-09 1,midg,midg; igrid,midg,midg -2.5578051E-09 1.8508532E-08 gauss-seidel spectral radius is 0.9873989 estimated iterations to convergence 73 setup time was (sec) 0.3900000 now iterating at: 07:51:16 rms-change max change #iterations 0.1421067 21.58771 at 10iterations 1.4552084E-02 2.192517 at 20iterations 1.5859123E-03 0.2463474 at 30iterations 2.2362049E-04 3.4147263E-02 at 40iterations 4.5248686E-05 7.0152283E-03 at 50iterations finished qdiffx linear iterations at : 07:51:19 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 4.5248686E-05 7.0152283E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 07:51:20 3.437u 0.175s 0:04.06 88.6% 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 07:51:20 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 = 2374 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.925434 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): -9.044000 36.56100 ymin,ymax (A): -14.63700 40.83100 zmin,zma (A): 5.167000 52.62900 x,y,z range (A): 45.60500 55.46800 47.46200 scale (grids/A): 1.925434 object centre (A): 13.75850 13.09700 28.89800 number of atom coordinates read : 2374 total number of charged atoms : 2238 net assigned charge : 4.500007 assigned positive charge : 356.5233 centred at (gu) : 91.50197 86.16862 92.08639 assigned negative charge : -352.0238 centred at (gu) : 91.23794 86.18813 92.52361 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 69242 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19885 grid for indexing accessible points = 1.400000 m= 26785 mr = 48216 m= 4691 mr = 20140 m= 318 mr = 3104 m= 7 mr = 126 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 299 time to turn everything in is 0.3700000 number of dielectric boundary points 29457 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 17597 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) : 0.6418115 object centre at (A) : 13.75850 13.09700 28.89800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6988568E-02 -2.1559665E-02 midg,1,midg; midg,igrid,midg 2.0144461E-02 3.4049783E-02 1,midg,midg; igrid,midg,midg -4.8661935E-03 7.7381604E-03 gauss-seidel spectral radius is 0.9986373 estimated iterations to convergence 215 setup time was (sec) 0.5800000 now iterating at: 07:51:21 rms-change max change #iterations 4.075235 206.9175 at 10iterations 1.913381 66.70651 at 20iterations 0.9033225 29.43418 at 30iterations 0.4209738 13.02118 at 40iterations 0.1993901 7.530426 at 50iterations 9.3500845E-02 3.053036 at 60iterations 4.4025846E-02 1.438712 at 70iterations 2.0651417E-02 0.6837940 at 80iterations 9.7131813E-03 0.3117790 at 90iterations 4.6103573E-03 0.1614161 at 100iterations 2.1878884E-03 7.5525761E-02 at 110iterations 1.0444453E-03 3.3798218E-02 at 120iterations finished qdiffx linear iterations at : 07:51:28 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 1.0444453E-03 3.3798218E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 07:51:28 7.907u 0.204s 0:08.40 96.4% 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 07:51:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2374 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: 2.888152 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): -9.044000 36.56100 ymin,ymax (A): -14.63700 40.83100 zmin,zma (A): 5.167000 52.62900 x,y,z range (A): 45.60500 55.46800 47.46200 scale (grids/A): 2.888152 object centre (A): 13.75850 13.09700 28.89800 number of atom coordinates read : 2374 total number of charged atoms : 2238 net assigned charge : 4.500007 assigned positive charge : 356.5233 centred at (gu) : 92.25286 84.25288 93.12952 assigned negative charge : -352.0238 centred at (gu) : 91.85688 84.28218 93.78532 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 159664 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19885 grid for indexing accessible points = 1.400000 m= 84324 mr = 116262 m= 33035 mr = 69727 m= 8551 mr = 27067 m= 1313 mr = 6581 m= 83 mr = 924 m= 4 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 1092 time to turn everything in is 0.9200000 number of dielectric boundary points 66365 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 17892 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) : 1.925434 object centre at (A) : 13.75850 13.09700 28.89800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4190536 -0.3071923 midg,1,midg; midg,igrid,midg 0.1376217 0.3375222 1,midg,midg; igrid,midg,midg -2.9135948E-02 1.1047071E-02 gauss-seidel spectral radius is 0.9992497 estimated iterations to convergence 288 setup time was (sec) 1.150000 now iterating at: 07:51:30 rms-change max change #iterations 9.529086 410.2988 at 10iterations 5.555705 128.3835 at 20iterations 3.223739 89.56446 at 30iterations 1.863103 34.99234 at 40iterations 1.074388 22.03262 at 50iterations 0.6187711 11.51760 at 60iterations 0.3561639 6.531719 at 70iterations 0.2044361 3.888607 at 80iterations 0.1174897 2.196683 at 90iterations 6.7216501E-02 1.162476 at 100iterations 3.8484283E-02 0.7441311 at 110iterations 2.2101378E-02 0.4122591 at 120iterations 1.2649431E-02 0.2457123 at 130iterations 7.2605913E-03 0.1514015 at 140iterations 4.1515469E-03 7.4106216E-02 at 150iterations 2.3791683E-03 4.4874191E-02 at 160iterations 1.3613168E-03 2.5384903E-02 at 170iterations 7.7974296E-04 1.4434814E-02 at 180iterations finished qdiffx linear iterations at : 07:51:41 total time elapsed so far: 12.61000 # loops : 180 mean,max change (kT/e) : 7.7974296E-04 1.4434814E-02 energy calculations done at 12.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 07:51:42 12.755u 0.224s 0:13.48 96.2% 0+0k 0+0io 0pf+0w