Sat Oct 8 11:48:12 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 Sat Oct 8 2011 at 11:48:12 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2533 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: 0.5957262 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): -13.25600 38.75900 ymin,ymax (A): 29.02300 74.60300 zmin,zma (A): -11.35600 48.40300 x,y,z range (A): 52.01500 45.58000 59.75900 scale (grids/A): 0.5957262 object centre (A): 12.75150 51.81300 18.52350 number of atom coordinates read : 2533 total number of charged atoms : 2385 net assigned charge : -1.999992 assigned positive charge : 370.3506 centred at (gu) : 89.97659 90.79720 90.84372 assigned negative charge : -372.3513 centred at (gu) : 89.97457 90.79300 90.74994 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5920 nv = 96 ne = 84 npr = 51265 no. pairs analyzed = 51265 no. exposed pairs = 3334 no. arc points = 23549 no. surface atoms = 1123 nbur = 1410 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 281 mr = 2971 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3213 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2346 ## 242 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7433 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.0277070E-09 2.5295044E-09 midg,1,midg; midg,igrid,midg -7.5392786E-10 -7.6570356E-10 1,midg,midg; igrid,midg,midg -8.3739693E-10 -7.0558170E-10 gauss-seidel spectral radius is 0.9854178 estimated iterations to convergence 68 setup time was (sec) 0.3900000 now iterating at: 11:48:13 rms-change max change #iterations 0.1027382 22.82489 at 10iterations 8.4568309E-03 1.395227 at 20iterations 6.9316127E-04 0.1216202 at 30iterations 5.8969370E-05 8.5639954E-03 at 40iterations 5.0321369E-06 7.5435638E-04 at 50iterations finished qdiffx linear iterations at : 11:48:17 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 5.0321369E-06 7.5435638E-04 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 11:48:18 3.426u 0.185s 0:05.96 60.4% 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 11:48:18 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2533 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: 1.787179 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): -13.25600 38.75900 ymin,ymax (A): 29.02300 74.60300 zmin,zma (A): -11.35600 48.40300 x,y,z range (A): 52.01500 45.58000 59.75900 scale (grids/A): 1.787179 object centre (A): 12.75150 51.81300 18.52350 number of atom coordinates read : 2533 total number of charged atoms : 2385 net assigned charge : -1.999992 assigned positive charge : 370.3506 centred at (gu) : 89.92914 92.39091 92.53061 assigned negative charge : -372.3513 centred at (gu) : 89.92348 92.37841 92.24946 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 64115 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23549 grid for indexing accessible points = 1.400000 m= 20971 mr = 42379 m= 2783 mr = 14565 m= 109 mr = 1481 m= 0 mr = 25 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 29528 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 219 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 18629 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) : 0.5957262 object centre at (A) : 12.75150 51.81300 18.52350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.6064314E-03 8.0671152E-03 midg,1,midg; midg,igrid,midg 7.2740193E-04 -6.8360134E-03 1,midg,midg; igrid,midg,midg -8.2468241E-03 -1.1648989E-02 gauss-seidel spectral radius is 0.9984502 estimated iterations to convergence 202 setup time was (sec) 0.5300000 now iterating at: 11:48:19 rms-change max change #iterations 3.610147 173.7962 at 10iterations 1.595319 60.35660 at 20iterations 0.7083209 23.60872 at 30iterations 0.3151789 10.52010 at 40iterations 0.1403039 5.095596 at 50iterations 6.2213395E-02 2.235867 at 60iterations 2.7766895E-02 1.010353 at 70iterations 1.2318764E-02 0.4582825 at 80iterations 5.4998412E-03 0.1855774 at 90iterations 2.4412449E-03 8.8937759E-02 at 100iterations 1.0926755E-03 4.0383339E-02 at 110iterations 4.8386035E-04 1.6264915E-02 at 120iterations finished qdiffx linear iterations at : 11:48:26 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 4.8386035E-04 1.6264915E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 11:48:27 7.868u 0.232s 0:08.94 90.4% 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 11:48:27 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2533 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: 2.680768 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): -13.25600 38.75900 ymin,ymax (A): 29.02300 74.60300 zmin,zma (A): -11.35600 48.40300 x,y,z range (A): 52.01500 45.58000 59.75900 scale (grids/A): 2.680768 object centre (A): 12.75150 51.81300 18.52350 number of atom coordinates read : 2533 total number of charged atoms : 2385 net assigned charge : -1.999992 assigned positive charge : 370.3506 centred at (gu) : 89.89355 93.58616 93.79558 assigned negative charge : -372.3513 centred at (gu) : 89.88502 93.56758 93.37424 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 148611 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23549 grid for indexing accessible points = 1.400000 m= 69142 mr = 103720 m= 22732 mr = 54412 m= 4556 mr = 17460 m= 482 mr = 3161 m= 17 mr = 276 m= 0 mr = 2 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 66509 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 19074 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) : 1.787179 object centre at (A) : 12.75150 51.81300 18.52350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8146824E-03 2.7196668E-02 midg,1,midg; midg,igrid,midg 1.8230921E-02 -0.1402319 1,midg,midg; igrid,midg,midg -9.0909205E-02 -0.1374649 gauss-seidel spectral radius is 0.9992109 estimated iterations to convergence 281 setup time was (sec) 1.070000 now iterating at: 11:48:28 rms-change max change #iterations 8.854906 321.2557 at 10iterations 5.105012 118.9061 at 20iterations 2.914973 73.96045 at 30iterations 1.659869 39.11666 at 40iterations 0.9420184 23.65015 at 50iterations 0.5335739 11.42740 at 60iterations 0.3016680 6.627889 at 70iterations 0.1706872 3.361405 at 80iterations 9.6497640E-02 1.973407 at 90iterations 5.4378819E-02 1.079224 at 100iterations 3.0708767E-02 0.6909828 at 110iterations 1.7318793E-02 0.3413177 at 120iterations 9.7687291E-03 0.1824195 at 130iterations 5.5066445E-03 0.1179810 at 140iterations 3.1067473E-03 6.4476967E-02 at 150iterations 1.7508463E-03 3.6148787E-02 at 160iterations 9.8873477E-04 2.1165848E-02 at 170iterations 5.5643875E-04 1.1238098E-02 at 180iterations finished qdiffx linear iterations at : 11:48:51 total time elapsed so far: 12.65000 # loops : 180 mean,max change (kT/e) : 5.5643875E-04 1.1238098E-02 energy calculations done at 12.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.78000 DelPhi exited at 11:48:52 12.780u 0.229s 0:24.77 52.4% 0+0k 0+0io 0pf+0w