Wed Feb 15 08:56:00 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:56:01 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 ! Automatically converted by prot2crg.py # of charge parameter records: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3273 !!! WARNING: DIC 166 has a net charge of -0.8000 !!! WARNING: HIY 168 has a net charge of 0.2000 !!! WARNING: DIC 255 has a net charge of -0.8000 !!! WARNING: ZN1 1075 has a net charge of 1.4000 !!! WARNING: ZN2 1078 has a net charge of 2.0000 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: 0.6030321 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): -59.73900 -10.23600 ymin,ymax (A): -5.553000 46.75200 zmin,zma (A): -68.73600 -9.700999 x,y,z range (A): 49.50300 52.30500 59.03500 scale (grids/A): 0.6030321 object centre (A): -34.98750 20.59950 -39.21850 number of atom coordinates read : 3273 total number of charged atoms : 3133 net assigned charge : -1.499957 assigned positive charge : 487.0540 centred at (gu) : 91.13331 89.34724 91.39588 assigned negative charge : -488.5550 centred at (gu) : 91.24194 89.54577 91.51466 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7654 nv = 96 ne = 84 npr = 68960 no. pairs analyzed = 68960 no. exposed pairs = 4052 no. arc points = 27367 no. surface atoms = 1387 nbur = 1886 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 394 mr = 4216 m= 0 mr = 46 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3786 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2649 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 9739 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8358392E-09 -9.1753369E-09 midg,1,midg; midg,igrid,midg 1.0641060E-08 -9.3012931E-09 1,midg,midg; igrid,midg,midg 3.6893109E-09 -7.9508329E-09 gauss-seidel spectral radius is 0.9858154 estimated iterations to convergence 69 setup time was (sec) 0.7000000 now iterating at: 08:56:01 rms-change max change #iterations 0.1258583 20.67623 at 10iterations 1.1113620E-02 1.682526 at 20iterations 1.3072742E-03 0.1868181 at 30iterations 4.2821726E-04 7.7566147E-02 at 40iterations 2.0442580E-04 3.6422729E-02 at 50iterations finished qdiffx linear iterations at : 08:56:05 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 2.0442580E-04 3.6422729E-02 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 08:56:06 4.237u 0.275s 0:05.97 75.3% 0+0k 0+0io 6pf+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 Wed Feb 15 2012 at 08:56:07 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 ! Automatically converted by prot2crg.py # of charge parameter records: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3273 !!! WARNING: DIC 166 has a net charge of -0.8000 !!! WARNING: HIY 168 has a net charge of 0.2000 !!! WARNING: DIC 255 has a net charge of -0.8000 !!! WARNING: ZN1 1075 has a net charge of 1.4000 !!! WARNING: ZN2 1078 has a net charge of 2.0000 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: 1.809096 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): -59.73900 -10.23600 ymin,ymax (A): -5.553000 46.75200 zmin,zma (A): -68.73600 -9.700999 x,y,z range (A): 49.50300 52.30500 59.03500 scale (grids/A): 1.809096 object centre (A): -34.98750 20.59950 -39.21850 number of atom coordinates read : 3273 total number of charged atoms : 3133 net assigned charge : -1.499957 assigned positive charge : 487.0540 centred at (gu) : 93.39912 88.04101 94.18701 assigned negative charge : -488.5550 centred at (gu) : 93.72556 88.63694 94.54330 start vw surface at 0.1700000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 84060 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27367 grid for indexing accessible points = 1.400000 m= 29254 mr = 59008 m= 4143 mr = 21228 m= 193 mr = 2486 m= 1 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 81 time to turn everything in is 0.7500000 number of dielectric boundary points 34862 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 198 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 24515 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) : 0.6030321 object centre at (A) : -34.98750 20.59950 -39.21850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3005458E-03 -2.1893349E-02 midg,1,midg; midg,igrid,midg 3.1155361E-02 -6.4687566E-03 1,midg,midg; igrid,midg,midg 1.3327933E-03 -2.7863601E-02 gauss-seidel spectral radius is 0.9985482 estimated iterations to convergence 208 setup time was (sec) 1.060000 now iterating at: 08:56:08 rms-change max change #iterations 4.373901 170.1779 at 10iterations 1.996474 73.86610 at 20iterations 0.9116215 27.71965 at 30iterations 0.4169290 13.28559 at 40iterations 0.1915348 5.700518 at 50iterations 8.7868400E-02 2.808521 at 60iterations 4.0470984E-02 1.236292 at 70iterations 1.8521680E-02 0.5553446 at 80iterations 8.6001391E-03 0.2631226 at 90iterations 4.1086199E-03 0.1441345 at 100iterations 2.0493751E-03 7.3821068E-02 at 110iterations 1.1419620E-03 4.3485641E-02 at 120iterations finished qdiffx linear iterations at : 08:56:16 total time elapsed so far: 9.660000 # loops : 120 mean,max change (kT/e) : 1.1419620E-03 4.3485641E-02 energy calculations done at 9.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.850000 DelPhi exited at 08:56:17 9.850u 0.318s 0:10.51 96.6% 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 Wed Feb 15 2012 at 08:56:17 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 ! Automatically converted by prot2crg.py # of charge parameter records: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3273 !!! WARNING: DIC 166 has a net charge of -0.8000 !!! WARNING: HIY 168 has a net charge of 0.2000 !!! WARNING: DIC 255 has a net charge of -0.8000 !!! WARNING: ZN1 1075 has a net charge of 1.4000 !!! WARNING: ZN2 1078 has a net charge of 2.0000 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: 2.713645 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): -59.73900 -10.23600 ymin,ymax (A): -5.553000 46.75200 zmin,zma (A): -68.73600 -9.700999 x,y,z range (A): 49.50300 52.30500 59.03500 scale (grids/A): 2.713645 object centre (A): -34.98750 20.59950 -39.21850 number of atom coordinates read : 3273 total number of charged atoms : 3133 net assigned charge : -1.499957 assigned positive charge : 487.0540 centred at (gu) : 95.09847 87.06137 96.28029 assigned negative charge : -488.5550 centred at (gu) : 95.58804 87.95525 96.81491 start vw surface at 0.1900000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 194568 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27367 grid for indexing accessible points = 1.400000 m= 96919 mr = 143368 m= 33115 mr = 78633 m= 7087 mr = 26064 m= 952 mr = 5284 m= 55 mr = 673 m= 0 mr = 25 time to grow re-entrant surface = 1.160000 no. cavity mid-points inaccessible to solvent = 332 time to turn everything in is 1.920000 number of dielectric boundary points 78649 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 2.080000 number of grid points assigned charge 25063 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) : 1.809096 object centre at (A) : -34.98750 20.59950 -39.21850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1983044E-02 -0.2201855 midg,1,midg; midg,igrid,midg 0.4313637 8.5815098E-03 1,midg,midg; igrid,midg,midg -7.7498755E-03 -0.3611346 gauss-seidel spectral radius is 0.9992426 estimated iterations to convergence 287 setup time was (sec) 2.260000 now iterating at: 08:56:20 rms-change max change #iterations 10.60616 335.8559 at 10iterations 6.246894 177.7838 at 20iterations 3.640548 97.08876 at 30iterations 2.113929 41.41968 at 40iterations 1.225520 25.36762 at 50iterations 0.7059606 13.75746 at 60iterations 0.4072675 7.357004 at 70iterations 0.2339539 4.230677 at 80iterations 0.1344827 2.332355 at 90iterations 7.7333130E-02 1.374006 at 100iterations 4.4359844E-02 0.8840518 at 110iterations 2.5527736E-02 0.4977627 at 120iterations 1.4679598E-02 0.2379616 at 130iterations 8.5035209E-03 0.1433792 at 140iterations 5.0016828E-03 0.1052914 at 150iterations 3.0294438E-03 6.4422607E-02 at 160iterations 1.9324003E-03 3.9676666E-02 at 170iterations 1.3375533E-03 3.0441284E-02 at 180iterations finished qdiffx linear iterations at : 08:56:34 total time elapsed so far: 16.64000 # loops : 180 mean,max change (kT/e) : 1.3375533E-03 3.0441284E-02 energy calculations done at 16.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.83000 DelPhi exited at 08:56:35 16.829u 0.343s 0:17.52 97.9% 0+0k 0+0io 0pf+0w