Sun Oct 9 23:47:46 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 Sun Oct 9 2011 at 23:47:46 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 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3133 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: 0.6028381 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): -28.41000 30.64400 ymin,ymax (A): 8.096001 62.14400 zmin,zma (A): 24.92500 77.29500 x,y,z range (A): 59.05400 54.04800 52.37000 scale (grids/A): 0.6028381 object centre (A): 1.117000 35.12000 51.11000 number of atom coordinates read : 3133 total number of charged atoms : 2988 net assigned charge : -0.4999911 assigned positive charge : 470.1989 centred at (gu) : 89.45019 89.00838 88.99223 assigned negative charge : -470.7002 centred at (gu) : 89.50186 89.01221 89.10953 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7600 nv = 96 ne = 84 npr = 62540 no. pairs analyzed = 62540 no. exposed pairs = 4066 no. arc points = 28824 no. surface atoms = 1360 nbur = 1773 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 380 mr = 4009 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.3100000 number of dielectric boundary points 3945 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2897 ## 320 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9565 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6569013E-09 -4.8012074E-09 midg,1,midg; midg,igrid,midg -1.5670583E-10 -3.9804610E-10 1,midg,midg; igrid,midg,midg 2.4600828E-09 -2.4856424E-09 gauss-seidel spectral radius is 0.9858078 estimated iterations to convergence 69 setup time was (sec) 0.5500000 now iterating at: 23:47:47 rms-change max change #iterations 0.1203342 16.56654 at 10iterations 1.0474362E-02 1.472363 at 20iterations 9.0824661E-04 0.1408138 at 30iterations 8.2317594E-05 1.1972785E-02 at 40iterations 1.0205904E-05 1.3180971E-03 at 50iterations finished qdiffx linear iterations at : 23:47:50 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.0205904E-05 1.3180971E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 23:47:50 3.426u 0.227s 0:03.95 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 Sun Oct 9 2011 at 23:47:50 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 = 3133 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: 1.808514 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): -28.41000 30.64400 ymin,ymax (A): 8.096001 62.14400 zmin,zma (A): 24.92500 77.29500 x,y,z range (A): 59.05400 54.04800 52.37000 scale (grids/A): 1.808514 object centre (A): 1.117000 35.12000 51.11000 number of atom coordinates read : 3133 total number of charged atoms : 2988 net assigned charge : -0.4999911 assigned positive charge : 470.1989 centred at (gu) : 88.34977 87.02469 86.97613 assigned negative charge : -470.7002 centred at (gu) : 88.50533 87.03647 87.32809 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 83264 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28824 grid for indexing accessible points = 1.400000 m= 27212 mr = 56685 m= 3610 mr = 19160 m= 137 mr = 1998 m= 0 mr = 28 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 396 time to turn everything in is 0.5800000 number of dielectric boundary points 36352 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 232 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 23310 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) : 0.6028381 object centre at (A) : 1.117000 35.12000 51.11000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.0183988E-03 -4.5363000E-03 midg,1,midg; midg,igrid,midg 8.2518011E-03 7.0524202E-03 1,midg,midg; igrid,midg,midg 9.0941172E-03 -1.1358955E-02 gauss-seidel spectral radius is 0.9985561 estimated iterations to convergence 209 setup time was (sec) 0.8800000 now iterating at: 23:47:52 rms-change max change #iterations 4.252227 174.1756 at 10iterations 1.931561 66.34151 at 20iterations 0.8862905 29.72201 at 30iterations 0.4041780 12.87716 at 40iterations 0.1857811 5.514513 at 50iterations 8.4599644E-02 2.807554 at 60iterations 3.8841024E-02 1.247353 at 70iterations 1.7824659E-02 0.5691290 at 80iterations 8.1754131E-03 0.2602348 at 90iterations 3.7292989E-03 0.1153450 at 100iterations 1.7099110E-03 5.6767464E-02 at 110iterations 7.8563608E-04 2.4396896E-02 at 120iterations finished qdiffx linear iterations at : 23:47:58 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 7.8563608E-04 2.4396896E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 23:47:59 7.858u 0.245s 0:08.41 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 Sun Oct 9 2011 at 23:47:59 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 = 3133 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: 2.712771 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): -28.41000 30.64400 ymin,ymax (A): 8.096001 62.14400 zmin,zma (A): 24.92500 77.29500 x,y,z range (A): 59.05400 54.04800 52.37000 scale (grids/A): 2.712771 object centre (A): 1.117000 35.12000 51.11000 number of atom coordinates read : 3133 total number of charged atoms : 2988 net assigned charge : -0.4999911 assigned positive charge : 470.1989 centred at (gu) : 87.52419 85.53672 85.46401 assigned negative charge : -470.7002 centred at (gu) : 87.75797 85.55444 85.99200 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 192997 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28824 grid for indexing accessible points = 1.400000 m= 91322 mr = 138095 m= 29033 mr = 72921 m= 5853 mr = 22300 m= 665 mr = 4207 m= 23 mr = 378 m= 0 mr = 3 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 1293 time to turn everything in is 1.400000 number of dielectric boundary points 81989 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 23903 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) : 1.808514 object centre at (A) : 1.117000 35.12000 51.11000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1296869 1.3743106E-02 midg,1,midg; midg,igrid,midg 5.0836459E-02 0.1160014 1,midg,midg; igrid,midg,midg 1.1097163E-02 -0.1432103 gauss-seidel spectral radius is 0.9992601 estimated iterations to convergence 290 setup time was (sec) 1.670000 now iterating at: 23:48:01 rms-change max change #iterations 10.43401 286.1810 at 10iterations 6.208319 146.8475 at 20iterations 3.654026 74.94128 at 30iterations 2.136114 44.08029 at 40iterations 1.250205 22.91357 at 50iterations 0.7259621 14.56729 at 60iterations 0.4216484 7.770427 at 70iterations 0.2439878 5.123538 at 80iterations 0.1411045 2.619806 at 90iterations 8.1698880E-02 1.475584 at 100iterations 4.7125295E-02 0.8565588 at 110iterations 2.7159441E-02 0.5893478 at 120iterations 1.5681531E-02 0.2957475 at 130iterations 9.0058763E-03 0.1620941 at 140iterations 5.1902542E-03 9.2351913E-02 at 150iterations 2.9895424E-03 5.2880287E-02 at 160iterations 1.7218768E-03 3.0149460E-02 at 170iterations 9.9059322E-04 1.6705990E-02 at 180iterations finished qdiffx linear iterations at : 23:48:10 total time elapsed so far: 11.08000 # loops : 180 mean,max change (kT/e) : 9.9059322E-04 1.6705990E-02 energy calculations done at 11.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.25000 DelPhi exited at 23:48:11 11.254u 0.212s 0:11.84 96.7% 0+0k 0+0io 0pf+0w