Sat Oct 8 12:26:04 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 Sat Oct 8 2011 at 12:26:04 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 = 3030 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: 0.5363950 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): -56.64800 9.721000 ymin,ymax (A): -38.14900 18.01200 zmin,zma (A): -4.229000 54.70700 x,y,z range (A): 66.36900 56.16100 58.93600 scale (grids/A): 0.5363950 object centre (A): -23.46350 -10.06850 25.23900 number of atom coordinates read : 3030 total number of charged atoms : 2892 net assigned charge : 1.000009 assigned positive charge : 416.4832 centred at (gu) : 92.61080 89.66986 89.56435 assigned negative charge : -415.4843 centred at (gu) : 92.47748 89.60641 89.52709 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6014 nv = 96 ne = 84 npr = 60722 no. pairs analyzed = 60722 no. exposed pairs = 4518 no. arc points = 32472 no. surface atoms = 1499 nbur = 1531 mkacc time = 0.1100000 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 = 1.596000 m= 250 mr = 2589 m= 2 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3670 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3089 ## 328 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7602 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4828162E-10 1.6686527E-10 midg,1,midg; midg,igrid,midg -2.6774280E-10 2.7300695E-10 1,midg,midg; igrid,midg,midg -2.8532032E-10 1.1568143E-09 gauss-seidel spectral radius is 0.9821157 estimated iterations to convergence 62 setup time was (sec) 0.4200000 now iterating at: 12:26:05 rms-change max change #iterations 6.2243145E-02 11.58583 at 10iterations 5.9072222E-03 1.194721 at 20iterations 1.8614612E-03 0.4175797 at 30iterations 7.5045560E-04 0.1699257 at 40iterations 3.0555620E-04 6.9412231E-02 at 50iterations finished qdiffx linear iterations at : 12:26:08 total time elapsed so far: 3.540000 # loops : 50 mean,max change (kT/e) : 3.0555620E-04 6.9412231E-02 energy calculations done at 3.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.670000 DelPhi exited at 12:26:09 3.678u 0.218s 0:04.21 92.1% 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 Sat Oct 8 2011 at 12:26:09 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 = 3030 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: 1.609185 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): -56.64800 9.721000 ymin,ymax (A): -38.14900 18.01200 zmin,zma (A): -4.229000 54.70700 x,y,z range (A): 66.36900 56.16100 58.93600 scale (grids/A): 1.609185 object centre (A): -23.46350 -10.06850 25.23900 number of atom coordinates read : 3030 total number of charged atoms : 2892 net assigned charge : 1.000009 assigned positive charge : 416.4832 centred at (gu) : 97.83166 89.00893 88.69191 assigned negative charge : -415.4843 centred at (gu) : 97.43208 88.81903 88.58109 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 65688 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32472 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 18707 mr = 40256 m= 1976 mr = 11201 m= 48 mr = 799 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 34162 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 237 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 22162 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) : 0.5363950 object centre at (A) : -23.46350 -10.06850 25.23900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9091060E-03 1.0308010E-02 midg,1,midg; midg,igrid,midg -3.9394712E-03 5.3790971E-03 1,midg,midg; igrid,midg,midg -2.0691596E-03 6.2801428E-03 gauss-seidel spectral radius is 0.9981641 estimated iterations to convergence 185 setup time was (sec) 0.5600000 now iterating at: 12:26:09 rms-change max change #iterations 3.062924 156.3437 at 10iterations 1.264566 52.40935 at 20iterations 0.5201268 19.12790 at 30iterations 0.2168882 8.949858 at 40iterations 8.9921936E-02 3.303236 at 50iterations 3.7582155E-02 1.435017 at 60iterations 1.6225794E-02 0.6529942 at 70iterations 7.5479955E-03 0.3427849 at 80iterations 3.9686523E-03 0.1890869 at 90iterations 2.4237421E-03 0.1117935 at 100iterations 1.6534633E-03 7.4901581E-02 at 110iterations 1.1789235E-03 5.3829193E-02 at 120iterations finished qdiffx linear iterations at : 12:26:17 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 1.1789235E-03 5.3829193E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.040000 DelPhi exited at 12:26:17 8.038u 0.207s 0:08.57 96.0% 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 Sat Oct 8 2011 at 12:26:17 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 = 3030 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: 2.413777 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): -56.64800 9.721000 ymin,ymax (A): -38.14900 18.01200 zmin,zma (A): -4.229000 54.70700 x,y,z range (A): 66.36900 56.16100 58.93600 scale (grids/A): 2.413777 object centre (A): -23.46350 -10.06850 25.23900 number of atom coordinates read : 3030 total number of charged atoms : 2892 net assigned charge : 1.000009 assigned positive charge : 416.4832 centred at (gu) : 101.7473 88.51306 88.03773 assigned negative charge : -415.4843 centred at (gu) : 101.1481 88.22845 87.87160 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 152374 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32472 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 64202 mr = 100376 m= 18081 mr = 46385 m= 2853 mr = 12148 m= 127 mr = 1618 m= 3 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8100000 number of dielectric boundary points 77091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 23110 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) : 1.609185 object centre at (A) : -23.46350 -10.06850 25.23900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3990569E-03 0.1641676 midg,1,midg; midg,igrid,midg -7.7095821E-02 8.1147350E-02 1,midg,midg; igrid,midg,midg -2.2480903E-02 9.6916743E-02 gauss-seidel spectral radius is 0.9991458 estimated iterations to convergence 270 setup time was (sec) 1.050000 now iterating at: 12:26:19 rms-change max change #iterations 8.259739 319.9510 at 10iterations 4.777248 135.9763 at 20iterations 2.728391 85.46533 at 30iterations 1.546353 38.35187 at 40iterations 0.8718344 21.81024 at 50iterations 0.4889167 11.68560 at 60iterations 0.2730684 6.291675 at 70iterations 0.1524213 3.561919 at 80iterations 8.4836714E-02 1.918197 at 90iterations 4.7202960E-02 1.050873 at 100iterations 2.6270362E-02 0.5798340 at 110iterations 1.4635072E-02 0.3124847 at 120iterations 8.1958110E-03 0.1708417 at 130iterations 4.6368190E-03 9.7194672E-02 at 140iterations 2.6865464E-03 6.3083649E-02 at 150iterations 1.6263700E-03 4.1778564E-02 at 160iterations 1.0498990E-03 2.6306152E-02 at 170iterations 7.3125307E-04 1.9950867E-02 at 180iterations finished qdiffx linear iterations at : 12:26:31 total time elapsed so far: 13.10000 # loops : 180 mean,max change (kT/e) : 7.3125307E-04 1.9950867E-02 energy calculations done at 13.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.24000 DelPhi exited at 12:26:31 13.240u 0.239s 0:13.76 97.8% 0+0k 0+0io 0pf+0w