Sat Oct 8 20:02:46 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 20:02:46 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2584 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 674 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6178839 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): -32.11900 17.57700 ymin,ymax (A): -24.27400 23.77000 zmin,zma (A): -12.46700 45.14900 x,y,z range (A): 49.69600 48.04400 57.61600 scale (grids/A): 0.6178839 object centre (A): -7.271000 -0.2519999 16.34100 number of atom coordinates read : 2584 total number of charged atoms : 2467 net assigned charge : 3.500007 assigned positive charge : 395.4800 centred at (gu) : 88.72471 89.19457 89.58474 assigned negative charge : -391.9806 centred at (gu) : 88.62336 89.24997 89.48300 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6358 nv = 96 ne = 84 npr = 53864 no. pairs analyzed = 53864 no. exposed pairs = 3025 no. arc points = 21604 no. surface atoms = 1006 nbur = 1578 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 317 mr = 3473 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 99 time to turn everything in is 0.2000000 number of dielectric boundary points 3168 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2242 ## 242 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8086 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1302699E-09 8.2693177E-09 midg,1,midg; midg,igrid,midg 7.4078144E-09 -6.2791133E-10 1,midg,midg; igrid,midg,midg -5.0273665E-09 6.8289805E-09 gauss-seidel spectral radius is 0.9864302 estimated iterations to convergence 70 setup time was (sec) 0.4000000 now iterating at: 20:02:46 rms-change max change #iterations 0.1243864 19.54888 at 10iterations 1.1374465E-02 1.669941 at 20iterations 1.0306714E-03 0.1443787 at 30iterations 9.4421834E-05 1.2207031E-02 at 40iterations 8.6162599E-06 1.2593269E-03 at 50iterations finished qdiffx linear iterations at : 20:02:51 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 8.6162599E-06 1.2593269E-03 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 20:02:51 3.555u 0.447s 0:05.67 70.3% 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 Sat Oct 8 2011 at 20:02:51 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2584 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 674 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.853652 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): -32.11900 17.57700 ymin,ymax (A): -24.27400 23.77000 zmin,zma (A): -12.46700 45.14900 x,y,z range (A): 49.69600 48.04400 57.61600 scale (grids/A): 1.853652 object centre (A): -7.271000 -0.2519999 16.34100 number of atom coordinates read : 2584 total number of charged atoms : 2467 net assigned charge : 3.500007 assigned positive charge : 395.4800 centred at (gu) : 86.17355 87.58345 88.75358 assigned negative charge : -391.9806 centred at (gu) : 85.87001 87.74992 88.44894 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 69540 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21604 grid for indexing accessible points = 1.400000 m= 23464 mr = 48321 m= 3224 mr = 17067 m= 133 mr = 1936 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 4799 time to turn everything in is 0.3600000 number of dielectric boundary points 29004 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 211 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 19353 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) : 0.6178839 object centre at (A) : -7.271000 -0.2519999 16.34100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3280630E-02 1.9693282E-02 midg,1,midg; midg,igrid,midg 1.2651885E-02 -1.5462523E-03 1,midg,midg; igrid,midg,midg -6.8314787E-04 3.7904344E-02 gauss-seidel spectral radius is 0.9985566 estimated iterations to convergence 209 setup time was (sec) 0.5800000 now iterating at: 20:02:52 rms-change max change #iterations 4.033594 174.8411 at 10iterations 1.843684 67.20368 at 20iterations 0.8447517 30.12006 at 30iterations 0.3885479 12.52969 at 40iterations 0.1785780 6.906517 at 50iterations 8.1828110E-02 2.894545 at 60iterations 3.7631791E-02 1.215162 at 70iterations 1.7199520E-02 0.5367517 at 80iterations 7.8714108E-03 0.2554951 at 90iterations 3.6013136E-03 0.1166916 at 100iterations 1.6592038E-03 5.1177979E-02 at 110iterations 7.5726048E-04 2.4366379E-02 at 120iterations finished qdiffx linear iterations at : 20:03:03 total time elapsed so far: 7.970000 # loops : 120 mean,max change (kT/e) : 7.5726048E-04 2.4366379E-02 energy calculations done at 7.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.120000 DelPhi exited at 20:03:04 8.122u 0.742s 0:12.35 71.7% 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 20:03:04 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2584 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 674 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.780478 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): -32.11900 17.57700 ymin,ymax (A): -24.27400 23.77000 zmin,zma (A): -12.46700 45.14900 x,y,z range (A): 49.69600 48.04400 57.61600 scale (grids/A): 2.780478 object centre (A): -7.271000 -0.2519999 16.34100 number of atom coordinates read : 2584 total number of charged atoms : 2467 net assigned charge : 3.500007 assigned positive charge : 395.4800 centred at (gu) : 84.26036 86.37499 88.13022 assigned negative charge : -391.9806 centred at (gu) : 83.80500 86.62479 87.67332 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 161389 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21604 grid for indexing accessible points = 1.400000 m= 77966 mr = 117380 m= 25592 mr = 63415 m= 5624 mr = 20321 m= 671 mr = 4185 m= 24 mr = 459 m= 0 mr = 3 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 16718 time to turn everything in is 0.9100000 number of dielectric boundary points 65503 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 19735 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) : 1.853652 object centre at (A) : -7.271000 -0.2519999 16.34100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3195403E-03 0.2551311 midg,1,midg; midg,igrid,midg 0.1513266 -2.7852247E-02 1,midg,midg; igrid,midg,midg -1.3755776E-02 0.5015300 gauss-seidel spectral radius is 0.9992315 estimated iterations to convergence 285 setup time was (sec) 1.160000 now iterating at: 20:03:06 rms-change max change #iterations 9.487758 281.9867 at 10iterations 5.437834 139.8094 at 20iterations 3.095198 72.09337 at 30iterations 1.762438 38.12923 at 40iterations 1.002706 20.08924 at 50iterations 0.5706617 13.21436 at 60iterations 0.3239460 6.196941 at 70iterations 0.1840338 3.508377 at 80iterations 0.1048095 2.057390 at 90iterations 5.9517603E-02 1.239506 at 100iterations 3.3766307E-02 0.6940918 at 110iterations 1.9175546E-02 0.3592682 at 120iterations 1.0904663E-02 0.2062569 at 130iterations 6.1876271E-03 0.1329412 at 140iterations 3.5133918E-03 7.3144913E-02 at 150iterations 1.9929290E-03 3.6876678E-02 at 160iterations 1.1327591E-03 2.2986412E-02 at 170iterations 6.4237515E-04 1.2119293E-02 at 180iterations finished qdiffx linear iterations at : 20:03:23 total time elapsed so far: 13.11000 # loops : 180 mean,max change (kT/e) : 6.4237515E-04 1.2119293E-02 energy calculations done at 13.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.26000 DelPhi exited at 20:03:23 13.260u 1.039s 0:19.42 73.5% 0+0k 0+0io 0pf+0w