Wed Feb 1 10:30:42 PST 2012 #!/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 Wed Feb 1 2012 at 10:30:42 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1965 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: 0.6086094 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): -8.894000 49.60000 ymin,ymax (A): -19.29000 19.93000 zmin,zma (A): -7.871000 34.70700 x,y,z range (A): 58.49400 39.22000 42.57800 scale (grids/A): 0.6086094 object centre (A): 20.35300 0.3200006 13.41800 number of atom coordinates read : 1965 total number of charged atoms : 1833 net assigned charge : 3.000003 assigned positive charge : 290.5330 centred at (gu) : 90.28216 90.36544 89.56400 assigned negative charge : -287.5333 centred at (gu) : 90.29170 90.48489 89.40223 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 4892 nv = 96 ne = 84 npr = 40108 no. pairs analyzed = 40108 no. exposed pairs = 2483 no. arc points = 17584 no. surface atoms = 841 nbur = 1124 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 216 mr = 2646 m= 0 mr = 9 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.1700000 number of dielectric boundary points 2453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1899 ## 253 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6039 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.4815307E-09 6.6489694E-09 midg,1,midg; midg,igrid,midg 5.4286922E-09 -2.7366891E-09 1,midg,midg; igrid,midg,midg 1.9595969E-09 1.5010027E-09 gauss-seidel spectral radius is 0.9859703 estimated iterations to convergence 69 setup time was (sec) 0.3600000 now iterating at: 10:30:42 rms-change max change #iterations 9.9145390E-02 17.37041 at 10iterations 8.6035077E-03 1.457840 at 20iterations 7.5171888E-04 0.1277618 at 30iterations 6.5056425E-05 1.4400482E-02 at 40iterations 5.7251114E-06 9.8800659E-04 at 50iterations finished qdiffx linear iterations at : 10:30:45 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 5.7251114E-06 9.8800659E-04 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 10:30:46 3.383u 0.183s 0:03.86 92.2% 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 Wed Feb 1 2012 at 10:30:46 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1965 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: 1.825828 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): -8.894000 49.60000 ymin,ymax (A): -19.29000 19.93000 zmin,zma (A): -7.871000 34.70700 x,y,z range (A): 58.49400 39.22000 42.57800 scale (grids/A): 1.825828 object centre (A): 20.35300 0.3200006 13.41800 number of atom coordinates read : 1965 total number of charged atoms : 1833 net assigned charge : 3.000003 assigned positive charge : 290.5330 centred at (gu) : 90.84625 91.09647 88.69244 assigned negative charge : -287.5333 centred at (gu) : 90.87537 91.45477 88.20686 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 53239 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17584 grid for indexing accessible points = 1.400000 m= 18199 mr = 36324 m= 2225 mr = 13497 m= 67 mr = 1316 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 1133 time to turn everything in is 0.2700000 number of dielectric boundary points 22584 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 182 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 14350 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) : 0.6086094 object centre at (A) : 20.35300 0.3200006 13.41800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.4956195E-03 1.1975496E-02 midg,1,midg; midg,igrid,midg 6.6332202E-03 -4.1614454E-03 1,midg,midg; igrid,midg,midg 3.3326395E-02 3.1183947E-02 gauss-seidel spectral radius is 0.9984394 estimated iterations to convergence 201 setup time was (sec) 0.4800000 now iterating at: 10:30:46 rms-change max change #iterations 3.314680 165.1740 at 10iterations 1.468099 60.08729 at 20iterations 0.6502773 24.20821 at 30iterations 0.2892574 10.57172 at 40iterations 0.1285863 4.657123 at 50iterations 5.7218794E-02 2.147083 at 60iterations 2.5256854E-02 0.8847733 at 70iterations 1.1250681E-02 0.4070338 at 80iterations 4.9834154E-03 0.1822681 at 90iterations 2.2233918E-03 8.4470749E-02 at 100iterations 9.8527560E-04 3.7078857E-02 at 110iterations 4.3737082E-04 1.7105103E-02 at 120iterations finished qdiffx linear iterations at : 10:30:54 total time elapsed so far: 7.510000 # loops : 120 mean,max change (kT/e) : 4.3737082E-04 1.7105103E-02 energy calculations done at 7.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 10:30:54 7.658u 0.255s 0:08.26 95.6% 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 Wed Feb 1 2012 at 10:30:54 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1965 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: 2.738742 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): -8.894000 49.60000 ymin,ymax (A): -19.29000 19.93000 zmin,zma (A): -7.871000 34.70700 x,y,z range (A): 58.49400 39.22000 42.57800 scale (grids/A): 2.738742 object centre (A): 20.35300 0.3200006 13.41800 number of atom coordinates read : 1965 total number of charged atoms : 1833 net assigned charge : 3.000003 assigned positive charge : 290.5330 centred at (gu) : 91.26945 91.64468 88.03875 assigned negative charge : -287.5333 centred at (gu) : 91.31303 92.18217 87.31042 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 123141 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17584 grid for indexing accessible points = 1.400000 m= 60500 mr = 88009 m= 19867 mr = 49741 m= 3726 mr = 15996 m= 326 mr = 2712 m= 7 mr = 170 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 3746 time to turn everything in is 0.6800000 number of dielectric boundary points 50939 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 14662 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) : 1.825828 object centre at (A) : 20.35300 0.3200006 13.41800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.4148543E-02 0.1089957 midg,1,midg; midg,igrid,midg 4.9052320E-02 -3.7124258E-02 1,midg,midg; igrid,midg,midg 0.3731280 0.3399237 gauss-seidel spectral radius is 0.9991876 estimated iterations to convergence 277 setup time was (sec) 0.9000000 now iterating at: 10:30:55 rms-change max change #iterations 7.939436 342.1752 at 10iterations 4.492698 119.4830 at 20iterations 2.526532 58.67341 at 30iterations 1.410097 31.16624 at 40iterations 0.7906759 17.82318 at 50iterations 0.4408264 10.53944 at 60iterations 0.2461536 5.350754 at 70iterations 0.1373816 3.142503 at 80iterations 7.6890975E-02 1.710064 at 90iterations 4.2860392E-02 0.9626517 at 100iterations 2.3832425E-02 0.5058098 at 110iterations 1.3324456E-02 0.2717297 at 120iterations 7.4307439E-03 0.1493607 at 130iterations 4.1537783E-03 8.6816788E-02 at 140iterations 2.3197599E-03 5.1741600E-02 at 150iterations 1.2915093E-03 2.7143478E-02 at 160iterations 7.1925926E-04 1.7301381E-02 at 170iterations 4.0150833E-04 8.6774826E-03 at 180iterations finished qdiffx linear iterations at : 10:31:06 total time elapsed so far: 11.86000 # loops : 180 mean,max change (kT/e) : 4.0150833E-04 8.6774826E-03 energy calculations done at 11.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.98000 DelPhi exited at 10:31:07 11.986u 0.280s 0:12.61 97.2% 0+0k 0+0io 0pf+0w