Mon Oct 10 16:32:06 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 Mon Oct 10 2011 at 16:32:06 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2383 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: 0.5833101 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): 201.7990 256.1230 ymin,ymax (A): 62.44400 106.3390 zmin,zma (A): 158.3620 219.3930 x,y,z range (A): 54.32399 43.89500 61.03101 scale (grids/A): 0.5833101 object centre (A): 228.9610 84.39150 188.8775 number of atom coordinates read : 2383 total number of charged atoms : 2246 net assigned charge : 12.50002 assigned positive charge : 361.7999 centred at (gu) : 90.89870 90.25079 90.00665 assigned negative charge : -349.3007 centred at (gu) : 91.02094 90.32433 89.98208 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5473 nv = 96 ne = 84 npr = 45725 no. pairs analyzed = 45725 no. exposed pairs = 3152 no. arc points = 23277 no. surface atoms = 1055 nbur = 1328 mkacc time = 9.9999994E-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 = 1.456000 m= 251 mr = 2678 m= 0 mr = 19 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3027 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2429 ## 309 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6869 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6125715E-09 3.5692782E-09 midg,1,midg; midg,igrid,midg 4.2464872E-09 1.7533542E-09 1,midg,midg; igrid,midg,midg 4.4066164E-09 8.2636503E-10 gauss-seidel spectral radius is 0.9847911 estimated iterations to convergence 67 setup time was (sec) 0.5200000 now iterating at: 16:32:06 rms-change max change #iterations 9.3172885E-02 19.61747 at 10iterations 7.2365915E-03 1.098480 at 20iterations 5.7292689E-04 0.1122017 at 30iterations 4.4242726E-05 7.2932243E-03 at 40iterations 3.5463759E-06 5.5718422E-04 at 50iterations finished qdiffx linear iterations at : 16:32:09 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 3.5463759E-06 5.5718422E-04 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 16:32:10 3.308u 0.181s 0:03.90 89.2% 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 Mon Oct 10 2011 at 16:32:10 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2383 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.749930 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): 201.7990 256.1230 ymin,ymax (A): 62.44400 106.3390 zmin,zma (A): 158.3620 219.3930 x,y,z range (A): 54.32399 43.89500 61.03101 scale (grids/A): 1.749930 object centre (A): 228.9610 84.39150 188.8775 number of atom coordinates read : 2383 total number of charged atoms : 2246 net assigned charge : 12.50002 assigned positive charge : 361.7999 centred at (gu) : 92.69551 90.75174 90.01931 assigned negative charge : -349.3007 centred at (gu) : 93.06286 90.97285 89.94602 start vw surface at 0.1600000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 59449 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23277 grid for indexing accessible points = 1.400000 m= 19022 mr = 38287 m= 2259 mr = 13345 m= 83 mr = 1205 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 391 time to turn everything in is 0.4500000 number of dielectric boundary points 27966 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 255 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 17491 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) : 0.5833101 object centre at (A) : 228.9610 84.39150 188.8775 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2181156E-04 3.2739513E-02 midg,1,midg; midg,igrid,midg 1.3562850E-02 9.3902219E-03 1,midg,midg; igrid,midg,midg 1.0194118E-02 9.2231873E-03 gauss-seidel spectral radius is 0.9983767 estimated iterations to convergence 197 setup time was (sec) 0.7200000 now iterating at: 16:32:11 rms-change max change #iterations 3.391730 176.8518 at 10iterations 1.479542 61.82365 at 20iterations 0.6416166 30.30787 at 30iterations 0.2803309 11.24220 at 40iterations 0.1220455 4.290866 at 50iterations 5.3436041E-02 2.036953 at 60iterations 2.3231665E-02 0.8770828 at 70iterations 1.0199858E-02 0.3949699 at 80iterations 4.4234232E-03 0.1638870 at 90iterations 1.9388854E-03 7.3929787E-02 at 100iterations 8.4688066E-04 3.1462908E-02 at 110iterations 3.6882973E-04 1.4237404E-02 at 120iterations finished qdiffx linear iterations at : 16:32:17 total time elapsed so far: 7.040000 # loops : 120 mean,max change (kT/e) : 3.6882973E-04 1.4237404E-02 energy calculations done at 7.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.210000 DelPhi exited at 16:32:18 7.214u 0.225s 0:07.86 94.5% 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 Mon Oct 10 2011 at 16:32:18 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2383 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: 2.624895 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): 201.7990 256.1230 ymin,ymax (A): 62.44400 106.3390 zmin,zma (A): 158.3620 219.3930 x,y,z range (A): 54.32399 43.89500 61.03101 scale (grids/A): 2.624895 object centre (A): 228.9610 84.39150 188.8775 number of atom coordinates read : 2383 total number of charged atoms : 2246 net assigned charge : 12.50002 assigned positive charge : 361.7999 centred at (gu) : 94.04314 91.12743 90.02878 assigned negative charge : -349.3007 centred at (gu) : 94.59414 91.45920 89.91895 start vw surface at 0.1400000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 137625 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23277 grid for indexing accessible points = 1.400000 m= 63474 mr = 93766 m= 19965 mr = 50256 m= 3762 mr = 15335 m= 360 mr = 2637 m= 9 mr = 194 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 1202 time to turn everything in is 1.010000 number of dielectric boundary points 63007 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 17957 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) : 1.749930 object centre at (A) : 228.9610 84.39150 188.8775 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5849046 0.3757495 midg,1,midg; midg,igrid,midg 0.1203363 0.1075133 1,midg,midg; igrid,midg,midg 0.1256385 0.1126760 gauss-seidel spectral radius is 0.9991886 estimated iterations to convergence 277 setup time was (sec) 1.310000 now iterating at: 16:32:19 rms-change max change #iterations 8.413065 296.7684 at 10iterations 4.809355 143.8424 at 20iterations 2.715025 63.40042 at 30iterations 1.527488 35.94440 at 40iterations 0.8562208 19.29936 at 50iterations 0.4805986 10.92102 at 60iterations 0.2679446 5.786646 at 70iterations 0.1498983 3.820641 at 80iterations 8.3584785E-02 1.808653 at 90iterations 4.6726923E-02 0.9735336 at 100iterations 2.6097178E-02 0.5575600 at 110iterations 1.4579883E-02 0.3077984 at 120iterations 8.1239929E-03 0.1638346 at 130iterations 4.5496952E-03 0.1028519 at 140iterations 2.5308002E-03 5.0897598E-02 at 150iterations 1.4145777E-03 3.0170441E-02 at 160iterations 7.8968098E-04 1.7470360E-02 at 170iterations 4.4109471E-04 9.1094971E-03 at 180iterations finished qdiffx linear iterations at : 16:32:28 total time elapsed so far: 10.64000 # loops : 180 mean,max change (kT/e) : 4.4109471E-04 9.1094971E-03 energy calculations done at 10.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.81000 DelPhi exited at 16:32:29 10.808u 0.216s 0:11.33 97.1% 0+0k 0+0io 0pf+0w