Tue Oct 11 04:31:55 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 Tue Oct 11 2011 at 04:31:55 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2730 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6419272 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): -11.41500 37.07200 ymin,ymax (A): -25.62800 22.60900 zmin,zma (A): -10.20700 45.25100 x,y,z range (A): 48.48700 48.23700 55.45800 scale (grids/A): 0.6419272 object centre (A): 12.82850 -1.509501 17.52200 number of atom coordinates read : 2730 total number of charged atoms : 2578 net assigned charge : 3.140013 assigned positive charge : 414.2298 centred at (gu) : 90.10268 90.28232 91.79199 assigned negative charge : -411.0903 centred at (gu) : 89.85424 90.10104 91.75487 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7401 nv = 96 ne = 84 npr = 56464 no. pairs analyzed = 56464 no. exposed pairs = 3297 no. arc points = 22985 no. surface atoms = 1126 nbur = 1604 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 398 mr = 4147 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3621 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2313 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 9053 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1619860E-11 1.3904343E-08 midg,1,midg; midg,igrid,midg -1.8159689E-08 2.9491135E-08 1,midg,midg; igrid,midg,midg -2.7825584E-08 3.6875377E-08 gauss-seidel spectral radius is 0.9874333 estimated iterations to convergence 73 setup time was (sec) 0.3900000 now iterating at: 04:31:56 rms-change max change #iterations 0.1535379 22.34347 at 10iterations 1.5662847E-02 2.603710 at 20iterations 1.6415060E-03 0.2568045 at 30iterations 1.7509071E-04 2.3399353E-02 at 40iterations 2.3230441E-05 3.6849976E-03 at 50iterations finished qdiffx linear iterations at : 04:31:58 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 2.3230441E-05 3.6849976E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 04:31:59 3.364u 0.177s 0:03.93 89.8% 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 Tue Oct 11 2011 at 04:31:59 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2730 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.925781 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): -11.41500 37.07200 ymin,ymax (A): -25.62800 22.60900 zmin,zma (A): -10.20700 45.25100 x,y,z range (A): 48.48700 48.23700 55.45800 scale (grids/A): 1.925781 object centre (A): 12.82850 -1.509501 17.52200 number of atom coordinates read : 2730 total number of charged atoms : 2578 net assigned charge : 3.140013 assigned positive charge : 414.2298 centred at (gu) : 90.30760 90.84643 95.37534 assigned negative charge : -411.0903 centred at (gu) : 89.56239 90.30287 95.26416 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 80159 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22985 grid for indexing accessible points = 1.400000 m= 29109 mr = 56387 m= 4279 mr = 21622 m= 240 mr = 2485 m= 1 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 656 time to turn everything in is 0.3900000 number of dielectric boundary points 33225 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 144 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 20304 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) : 0.6419272 object centre at (A) : 12.82850 -1.509501 17.52200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8243693E-02 7.6440433E-03 midg,1,midg; midg,igrid,midg -1.3818756E-02 3.0369302E-02 1,midg,midg; igrid,midg,midg -6.4173001E-03 5.6477252E-02 gauss-seidel spectral radius is 0.9986749 estimated iterations to convergence 218 setup time was (sec) 0.6100000 now iterating at: 04:32:00 rms-change max change #iterations 4.479960 205.8996 at 10iterations 2.126030 80.95905 at 20iterations 1.009259 35.30745 at 30iterations 0.4786903 18.08330 at 40iterations 0.2267395 6.891365 at 50iterations 0.1072363 3.583847 at 60iterations 5.1030427E-02 1.530117 at 70iterations 2.4181020E-02 0.7340508 at 80iterations 1.1439690E-02 0.3734875 at 90iterations 5.4464233E-03 0.1702614 at 100iterations 2.5780967E-03 8.9279175E-02 at 110iterations 1.2258005E-03 4.2033195E-02 at 120iterations finished qdiffx linear iterations at : 04:32:07 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 1.2258005E-03 4.2033195E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 04:32:07 7.826u 0.198s 0:08.38 95.5% 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 Tue Oct 11 2011 at 04:32:07 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2730 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.888672 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): -11.41500 37.07200 ymin,ymax (A): -25.62800 22.60900 zmin,zma (A): -10.20700 45.25100 x,y,z range (A): 48.48700 48.23700 55.45800 scale (grids/A): 2.888672 object centre (A): 12.82850 -1.509501 17.52200 number of atom coordinates read : 2730 total number of charged atoms : 2578 net assigned charge : 3.140013 assigned positive charge : 414.2298 centred at (gu) : 90.46120 91.26962 98.06299 assigned negative charge : -411.0903 centred at (gu) : 89.34364 90.45425 97.89611 start vw surface at 0.1000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 185145 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22985 grid for indexing accessible points = 1.400000 m= 94726 mr = 136175 m= 33617 mr = 78074 m= 7708 mr = 26916 m= 1050 mr = 5536 m= 59 mr = 689 m= 0 mr = 21 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 2227 time to turn everything in is 1.030000 number of dielectric boundary points 74894 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 20620 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) : 1.925781 object centre at (A) : 12.82850 -1.509501 17.52200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4202360 0.3202683 midg,1,midg; midg,igrid,midg -0.1652869 0.3460346 1,midg,midg; igrid,midg,midg -8.9078099E-03 0.5003157 gauss-seidel spectral radius is 0.9992675 estimated iterations to convergence 292 setup time was (sec) 1.280000 now iterating at: 04:32:09 rms-change max change #iterations 10.52209 354.5132 at 10iterations 6.179258 126.4296 at 20iterations 3.601392 80.61176 at 30iterations 2.100782 39.34435 at 40iterations 1.221619 24.77892 at 50iterations 0.7083118 13.87208 at 60iterations 0.4101755 7.300491 at 70iterations 0.2380286 4.838791 at 80iterations 0.1375654 2.498350 at 90iterations 7.9641581E-02 1.336801 at 100iterations 4.6082634E-02 0.8121681 at 110iterations 2.6669564E-02 0.4538155 at 120iterations 1.5429762E-02 0.2937948 at 130iterations 8.9498367E-03 0.1504707 at 140iterations 5.1773344E-03 8.7954521E-02 at 150iterations 3.0173601E-03 5.5534840E-02 at 160iterations 1.7649564E-03 3.2825470E-02 at 170iterations 1.0407955E-03 2.3448944E-02 at 180iterations finished qdiffx linear iterations at : 04:32:20 total time elapsed so far: 12.62000 # loops : 180 mean,max change (kT/e) : 1.0407955E-03 2.3448944E-02 energy calculations done at 12.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 04:32:21 12.757u 0.180s 0:13.22 97.8% 0+0k 0+0io 0pf+0w