Mon Oct 10 17:04:01 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 Mon Oct 10 2011 at 17:04:01 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3180 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: HIR 148 has a net charge of 0.5140 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: 0.5914112 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): -8.967000 48.87800 ymin,ymax (A): -7.925000 43.85100 zmin,zma (A): -4.698000 55.49700 x,y,z range (A): 57.84500 51.77600 60.19500 scale (grids/A): 0.5914112 object centre (A): 19.95550 17.96300 25.39950 number of atom coordinates read : 3180 total number of charged atoms : 3038 net assigned charge : -2.971960 assigned positive charge : 484.5375 centred at (gu) : 89.74239 88.39060 89.18362 assigned negative charge : -487.5108 centred at (gu) : 89.70950 88.31011 89.07648 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7336 nv = 96 ne = 84 npr = 64165 no. pairs analyzed = 64165 no. exposed pairs = 4065 no. arc points = 28515 no. surface atoms = 1379 nbur = 1801 mkacc time = 0.1300000 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 = 1.456000 m= 290 mr = 3863 m= 2 mr = 18 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 3747 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2899 ## 357 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9293 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.6187144E-09 2.3270086E-09 midg,1,midg; midg,igrid,midg -5.3825762E-09 1.3063581E-09 1,midg,midg; igrid,midg,midg -2.1368873E-09 2.5903052E-10 gauss-seidel spectral radius is 0.9852579 estimated iterations to convergence 68 setup time was (sec) 0.5500000 now iterating at: 17:04:02 rms-change max change #iterations 0.1188119 18.68333 at 10iterations 9.6675465E-03 1.526337 at 20iterations 7.8215043E-04 0.1121035 at 30iterations 6.5709857E-05 1.0934830E-02 at 40iterations 5.5174437E-06 7.7056885E-04 at 50iterations finished qdiffx linear iterations at : 17:04:05 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 5.5174437E-06 7.7056885E-04 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.200000 DelPhi exited at 17:04:06 3.203u 0.178s 0:04.09 82.3% 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 17:04:06 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3180 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: HIR 148 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.774234 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): -8.967000 48.87800 ymin,ymax (A): -7.925000 43.85100 zmin,zma (A): -4.698000 55.49700 x,y,z range (A): 57.84500 51.77600 60.19500 scale (grids/A): 1.774234 object centre (A): 19.95550 17.96300 25.39950 number of atom coordinates read : 3180 total number of charged atoms : 3038 net assigned charge : -2.971960 assigned positive charge : 484.5375 centred at (gu) : 89.22606 85.17097 87.54987 assigned negative charge : -487.5108 centred at (gu) : 89.12814 84.92966 87.22919 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 79980 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28515 grid for indexing accessible points = 1.400000 m= 25675 mr = 54361 m= 3050 mr = 17974 m= 127 mr = 1612 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1019 time to turn everything in is 0.5600000 number of dielectric boundary points 34866 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 302 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 23654 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) : 0.5914112 object centre at (A) : 19.95550 17.96300 25.39950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3199122E-02 -3.9179060E-03 midg,1,midg; midg,igrid,midg -2.4039412E-02 2.0026912E-03 1,midg,midg; igrid,midg,midg -3.6118131E-02 1.1373599E-02 gauss-seidel spectral radius is 0.9984865 estimated iterations to convergence 204 setup time was (sec) 0.8300000 now iterating at: 17:04:07 rms-change max change #iterations 4.215999 165.4895 at 10iterations 1.882170 62.11743 at 20iterations 0.8448797 28.81172 at 30iterations 0.3803992 12.88906 at 40iterations 0.1711959 5.784595 at 50iterations 7.6847121E-02 2.461052 at 60iterations 3.4414582E-02 1.046751 at 70iterations 1.5513059E-02 0.5231875 at 80iterations 6.9652135E-03 0.2324142 at 90iterations 3.1383745E-03 0.1054134 at 100iterations 1.4121481E-03 4.3495178E-02 at 110iterations 6.3684251E-04 2.0994425E-02 at 120iterations finished qdiffx linear iterations at : 17:04:13 total time elapsed so far: 6.950000 # loops : 120 mean,max change (kT/e) : 6.3684251E-04 2.0994425E-02 energy calculations done at 6.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.140000 DelPhi exited at 17:04:15 7.144u 0.196s 0:09.33 78.5% 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 17:04:15 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3180 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: HIR 148 has a net charge of 0.5140 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: 2.661351 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): -8.967000 48.87800 ymin,ymax (A): -7.925000 43.85100 zmin,zma (A): -4.698000 55.49700 x,y,z range (A): 57.84500 51.77600 60.19500 scale (grids/A): 2.661351 object centre (A): 19.95550 17.96300 25.39950 number of atom coordinates read : 3180 total number of charged atoms : 3038 net assigned charge : -2.971960 assigned positive charge : 484.5375 centred at (gu) : 88.83891 82.75620 86.32452 assigned negative charge : -487.5108 centred at (gu) : 88.69209 82.39449 85.84374 start vw surface at 0.1700000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 185404 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28515 grid for indexing accessible points = 1.400000 m= 86884 mr = 132544 m= 26773 mr = 69301 m= 4969 mr = 20507 m= 549 mr = 3367 m= 24 mr = 291 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 3424 time to turn everything in is 1.360000 number of dielectric boundary points 78593 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 24297 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) : 1.774234 object centre at (A) : 19.95550 17.96300 25.39950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2497964 -0.3414184 midg,1,midg; midg,igrid,midg -0.2640357 2.3260377E-02 1,midg,midg; igrid,midg,midg -0.4541347 0.2181172 gauss-seidel spectral radius is 0.9992375 estimated iterations to convergence 286 setup time was (sec) 1.640000 now iterating at: 17:04:17 rms-change max change #iterations 10.33371 411.8275 at 10iterations 6.032412 153.1555 at 20iterations 3.475505 76.93272 at 30iterations 1.996590 45.98893 at 40iterations 1.148161 21.62743 at 50iterations 0.6576695 13.77327 at 60iterations 0.3757224 7.166037 at 70iterations 0.2143439 4.019488 at 80iterations 0.1223189 2.236935 at 90iterations 6.9666602E-02 1.238981 at 100iterations 3.9701030E-02 0.6957703 at 110iterations 2.2587121E-02 0.4206820 at 120iterations 1.2857929E-02 0.2321558 at 130iterations 7.3197284E-03 0.1231689 at 140iterations 4.1637793E-03 7.9387665E-02 at 150iterations 2.3744837E-03 4.1313171E-02 at 160iterations 1.3478770E-03 2.4093628E-02 at 170iterations 7.6845766E-04 1.4045715E-02 at 180iterations finished qdiffx linear iterations at : 17:04:26 total time elapsed so far: 11.13000 # loops : 180 mean,max change (kT/e) : 7.6845766E-04 1.4045715E-02 energy calculations done at 11.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.31000 DelPhi exited at 17:04:28 11.314u 0.218s 0:12.63 91.2% 0+0k 0+0io 0pf+0w