Mon Oct 10 09:50:51 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 Mon Oct 10 2011 at 09:50:51 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 = 2804 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5836927 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): -17.04000 36.39000 ymin,ymax (A): -64.74600 -4.804000 zmin,zma (A): -3.715000 57.27600 x,y,z range (A): 53.43000 59.94200 60.99100 scale (grids/A): 0.5836927 object centre (A): 9.674999 -34.77500 26.78050 number of atom coordinates read : 2804 total number of charged atoms : 2653 net assigned charge : 8.000018 assigned positive charge : 409.4210 centred at (gu) : 88.79649 89.74836 87.33311 assigned negative charge : -401.4214 centred at (gu) : 88.89394 89.67918 87.23747 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6406 nv = 96 ne = 84 npr = 54769 no. pairs analyzed = 54769 no. exposed pairs = 4293 no. arc points = 31724 no. surface atoms = 1408 nbur = 1396 mkacc time = 0.1200000 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 = 1.484000 m= 324 mr = 2719 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3991 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3144 ## 352 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8129 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8792392E-10 2.2384119E-09 midg,1,midg; midg,igrid,midg 4.8047738E-10 3.3328587E-09 1,midg,midg; igrid,midg,midg 5.4897016E-09 -1.1578766E-10 gauss-seidel spectral radius is 0.9848528 estimated iterations to convergence 67 setup time was (sec) 0.5100000 now iterating at: 09:50:51 rms-change max change #iterations 9.3380824E-02 13.24060 at 10iterations 7.2952653E-03 1.291812 at 20iterations 6.0042326E-04 0.1031750 at 30iterations 6.0144717E-05 9.5357895E-03 at 40iterations 9.5120604E-06 1.0871887E-03 at 50iterations finished qdiffx linear iterations at : 09:50:54 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 9.5120604E-06 1.0871887E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 09:50:54 3.129u 0.145s 0:03.60 90.5% 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 09:50:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2804 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: 1.751078 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): -17.04000 36.39000 ymin,ymax (A): -64.74600 -4.804000 zmin,zma (A): -3.715000 57.27600 x,y,z range (A): 53.43000 59.94200 60.99100 scale (grids/A): 1.751078 object centre (A): 9.674999 -34.77500 26.78050 number of atom coordinates read : 2804 total number of charged atoms : 2653 net assigned charge : 8.000018 assigned positive charge : 409.4210 centred at (gu) : 86.38913 89.24482 81.99894 assigned negative charge : -401.4214 centred at (gu) : 86.68163 89.03696 81.71204 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 68244 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31724 grid for indexing accessible points = 1.400000 m= 21933 mr = 41002 m= 3038 mr = 13844 m= 125 mr = 1463 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 37020 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 277 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 20657 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) : 0.5836927 object centre at (A) : 9.674999 -34.77500 26.78050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0739154E-04 4.2690434E-03 midg,1,midg; midg,igrid,midg 2.4727738E-02 4.2126473E-02 1,midg,midg; igrid,midg,midg 1.9370604E-02 5.2384795E-03 gauss-seidel spectral radius is 0.9984322 estimated iterations to convergence 200 setup time was (sec) 0.7600000 now iterating at: 09:50:55 rms-change max change #iterations 3.697019 165.1887 at 10iterations 1.632681 62.11497 at 20iterations 0.7199534 25.23675 at 30iterations 0.3183646 10.77274 at 40iterations 0.1410224 5.352707 at 50iterations 6.2057272E-02 2.008449 at 60iterations 2.7511315E-02 0.9925423 at 70iterations 1.2130152E-02 0.4582977 at 80iterations 5.3680972E-03 0.1793733 at 90iterations 2.3888098E-03 8.1335068E-02 at 100iterations 1.0567876E-03 3.6712646E-02 at 110iterations 4.6852103E-04 1.5824318E-02 at 120iterations finished qdiffx linear iterations at : 09:51:01 total time elapsed so far: 6.680000 # loops : 120 mean,max change (kT/e) : 4.6852103E-04 1.5824318E-02 energy calculations done at 6.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.860000 DelPhi exited at 09:51:02 6.859u 0.162s 0:07.29 96.1% 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 Mon Oct 10 2011 at 09:51:02 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 = 2804 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: 2.626617 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): -17.04000 36.39000 ymin,ymax (A): -64.74600 -4.804000 zmin,zma (A): -3.715000 57.27600 x,y,z range (A): 53.43000 59.94200 60.99100 scale (grids/A): 2.626617 object centre (A): 9.674999 -34.77500 26.78050 number of atom coordinates read : 2804 total number of charged atoms : 2653 net assigned charge : 8.000018 assigned positive charge : 409.4210 centred at (gu) : 84.58354 88.86691 77.99831 assigned negative charge : -401.4214 centred at (gu) : 85.02223 88.55546 77.56809 start vw surface at 0.1400000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 157592 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31724 grid for indexing accessible points = 1.400000 m= 71109 mr = 101448 m= 23737 mr = 52397 m= 5041 mr = 17237 m= 547 mr = 3149 m= 16 mr = 229 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.180000 number of dielectric boundary points 83582 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 21220 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) : 1.751078 object centre at (A) : 9.674999 -34.77500 26.78050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0119612E-02 4.0826965E-02 midg,1,midg; midg,igrid,midg 0.6107160 0.4975702 1,midg,midg; igrid,midg,midg 0.1662433 7.9426408E-02 gauss-seidel spectral radius is 0.9992312 estimated iterations to convergence 285 setup time was (sec) 1.460000 now iterating at: 09:51:03 rms-change max change #iterations 9.363890 336.7456 at 10iterations 5.547935 160.0532 at 20iterations 3.234278 90.38618 at 30iterations 1.875478 46.94865 at 40iterations 1.082421 27.04261 at 50iterations 0.6234944 18.34820 at 60iterations 0.3568896 8.140772 at 70iterations 0.2041095 5.392357 at 80iterations 0.1166644 2.981094 at 90iterations 6.6550158E-02 1.398949 at 100iterations 3.7902225E-02 0.7853050 at 110iterations 2.1627530E-02 0.4817524 at 120iterations 1.2263858E-02 0.2670317 at 130iterations 6.9785588E-03 0.1390438 at 140iterations 3.9656642E-03 7.7398300E-02 at 150iterations 2.2526912E-03 4.3984413E-02 at 160iterations 1.2804632E-03 3.0925751E-02 at 170iterations 7.2856044E-04 1.5328884E-02 at 180iterations finished qdiffx linear iterations at : 09:51:13 total time elapsed so far: 10.90000 # loops : 180 mean,max change (kT/e) : 7.2856044E-04 1.5328884E-02 energy calculations done at 10.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.06000 DelPhi exited at 09:51:13 11.065u 0.184s 0:11.56 97.2% 0+0k 0+0io 0pf+0w