Tue Oct 11 08:22:06 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 Tue Oct 11 2011 at 08:22:06 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2792 !!! WARNING: SER 51 has a net charge of 0.5000 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6451262 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): -10.95900 37.41700 ymin,ymax (A): -26.99900 21.48800 zmin,zma (A): -9.696000 45.48700 x,y,z range (A): 48.37600 48.48700 55.18300 scale (grids/A): 0.6451262 object centre (A): 13.22900 -2.755501 17.89550 number of atom coordinates read : 2792 total number of charged atoms : 2639 net assigned charge : 3.662021 assigned positive charge : 420.8557 centred at (gu) : 89.70746 90.49442 91.57799 assigned negative charge : -417.1943 centred at (gu) : 89.48076 90.32314 91.56289 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7642 nv = 96 ne = 84 npr = 57424 no. pairs analyzed = 57424 no. exposed pairs = 3326 no. arc points = 22884 no. surface atoms = 1123 nbur = 1669 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 387 mr = 4373 m= 3 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2262 ## 235 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9273 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9152318E-09 1.1581350E-08 midg,1,midg; midg,igrid,midg -1.6964542E-08 3.3696463E-08 1,midg,midg; igrid,midg,midg -2.9039839E-08 3.5622264E-08 gauss-seidel spectral radius is 0.9875615 estimated iterations to convergence 73 setup time was (sec) 0.5700000 now iterating at: 08:22:07 rms-change max change #iterations 0.1556566 22.49930 at 10iterations 1.5765918E-02 2.380730 at 20iterations 1.6504506E-03 0.2215424 at 30iterations 1.8542365E-04 3.1023026E-02 at 40iterations 2.4737617E-05 3.8986206E-03 at 50iterations finished qdiffx linear iterations at : 08:22:10 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 2.4737617E-05 3.8986206E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 08:22:10 3.347u 0.136s 0:03.90 88.9% 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 08:22:10 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2792 !!! WARNING: SER 51 has a net charge of 0.5000 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.935379 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): -10.95900 37.41700 ymin,ymax (A): -26.99900 21.48800 zmin,zma (A): -9.696000 45.48700 x,y,z range (A): 48.37600 48.48700 55.18300 scale (grids/A): 1.935379 object centre (A): 13.22900 -2.755501 17.89550 number of atom coordinates read : 2792 total number of charged atoms : 2639 net assigned charge : 3.662021 assigned positive charge : 420.8557 centred at (gu) : 89.12198 91.48277 94.73332 assigned negative charge : -417.1943 centred at (gu) : 88.44164 90.96903 94.68839 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 82593 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22884 grid for indexing accessible points = 1.400000 m= 31037 mr = 58609 m= 4900 mr = 23491 m= 273 mr = 3078 m= 1 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1005 time to turn everything in is 0.6200000 number of dielectric boundary points 33540 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 163 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 20827 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) : 0.6451262 object centre at (A) : 13.22900 -2.755501 17.89550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0729974E-02 1.0883064E-02 midg,1,midg; midg,igrid,midg -1.1003978E-02 2.2856681E-02 1,midg,midg; igrid,midg,midg -1.4635405E-02 5.4977216E-02 gauss-seidel spectral radius is 0.9986919 estimated iterations to convergence 219 setup time was (sec) 0.9300000 now iterating at: 08:22:11 rms-change max change #iterations 4.542882 235.9995 at 10iterations 2.162693 67.19597 at 20iterations 1.033501 32.52657 at 30iterations 0.4920328 15.27443 at 40iterations 0.2343431 6.761168 at 50iterations 0.1118044 3.440461 at 60iterations 5.3536016E-02 1.665214 at 70iterations 2.5421185E-02 0.7400322 at 80iterations 1.2121280E-02 0.3537407 at 90iterations 5.7709632E-03 0.1893396 at 100iterations 2.7634278E-03 7.9960465E-02 at 110iterations 1.3149454E-03 4.5502663E-02 at 120iterations finished qdiffx linear iterations at : 08:22:18 total time elapsed so far: 7.980000 # loops : 120 mean,max change (kT/e) : 1.3149454E-03 4.5502663E-02 energy calculations done at 7.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.170000 DelPhi exited at 08:22:19 8.173u 0.208s 0:08.71 96.0% 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 08:22:19 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2792 !!! WARNING: SER 51 has a net charge of 0.5000 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.903068 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): -10.95900 37.41700 ymin,ymax (A): -26.99900 21.48800 zmin,zma (A): -9.696000 45.48700 x,y,z range (A): 48.37600 48.48700 55.18300 scale (grids/A): 2.903068 object centre (A): 13.22900 -2.755501 17.89550 number of atom coordinates read : 2792 total number of charged atoms : 2639 net assigned charge : 3.662021 assigned positive charge : 420.8557 centred at (gu) : 88.68298 92.22404 97.09990 assigned negative charge : -417.1943 centred at (gu) : 87.66243 91.45360 97.03271 start vw surface at 0.1800000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 190901 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22884 grid for indexing accessible points = 1.400000 m= 99963 mr = 141461 m= 36548 mr = 83196 m= 8814 mr = 29797 m= 1268 mr = 6704 m= 70 mr = 830 m= 5 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.9200001 no. cavity mid-points inaccessible to solvent = 3466 time to turn everything in is 1.590000 number of dielectric boundary points 75542 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 21112 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) : 1.935379 object centre at (A) : 13.22900 -2.755501 17.89550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3843675 0.3364834 midg,1,midg; midg,igrid,midg -0.1361693 0.2240730 1,midg,midg; igrid,midg,midg -0.1585763 0.4970982 gauss-seidel spectral radius is 0.9992707 estimated iterations to convergence 292 setup time was (sec) 1.900000 now iterating at: 08:22:21 rms-change max change #iterations 10.53612 418.9465 at 10iterations 6.177746 154.0856 at 20iterations 3.604472 79.18304 at 30iterations 2.100959 39.69343 at 40iterations 1.224445 25.44727 at 50iterations 0.7110260 14.26449 at 60iterations 0.4123261 7.918856 at 70iterations 0.2385896 4.339689 at 80iterations 0.1382976 2.402657 at 90iterations 8.0209769E-02 1.447279 at 100iterations 4.6406321E-02 0.8516648 at 110iterations 2.6903961E-02 0.4580097 at 120iterations 1.5526635E-02 0.2882690 at 130iterations 9.0059144E-03 0.1677971 at 140iterations 5.2188099E-03 9.2126846E-02 at 150iterations 3.0346762E-03 6.0567856E-02 at 160iterations 1.7671698E-03 3.7059784E-02 at 170iterations 1.0366888E-03 1.9157410E-02 at 180iterations finished qdiffx linear iterations at : 08:22:31 total time elapsed so far: 12.21000 # loops : 180 mean,max change (kT/e) : 1.0366888E-03 1.9157410E-02 energy calculations done at 12.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.43000 DelPhi exited at 08:22:32 12.433u 0.204s 0:13.21 95.6% 0+0k 0+0io 0pf+0w