Sat Oct 8 21:15:20 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 21:15:20 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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: ZN4 492 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6291976 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): -31.62100 17.49900 ymin,ymax (A): -23.63100 22.66200 zmin,zma (A): -12.44700 44.13300 x,y,z range (A): 49.12000 46.29300 56.58000 scale (grids/A): 0.6291976 object centre (A): -7.061000 -0.4845009 15.84300 number of atom coordinates read : 2594 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 392.2440 centred at (gu) : 88.51527 89.32309 89.90633 assigned negative charge : -388.3386 centred at (gu) : 88.42712 89.36922 89.78541 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6645 nv = 96 ne = 84 npr = 55403 no. pairs analyzed = 55403 no. exposed pairs = 2970 no. arc points = 21236 no. surface atoms = 1001 nbur = 1593 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 307 mr = 3710 m= 4 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 134 time to turn everything in is 0.3100000 number of dielectric boundary points 3201 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2101 ## 205 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8214 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.4553434E-09 1.4256782E-08 midg,1,midg; midg,igrid,midg 9.5137578E-09 2.4841185E-10 1,midg,midg; igrid,midg,midg -4.8776063E-09 8.5608756E-09 gauss-seidel spectral radius is 0.9869080 estimated iterations to convergence 71 setup time was (sec) 0.5500000 now iterating at: 21:15:21 rms-change max change #iterations 0.1351959 20.18240 at 10iterations 1.2966030E-02 2.102554 at 20iterations 1.2537803E-03 0.1837006 at 30iterations 1.1804419E-04 1.6752243E-02 at 40iterations 1.1401637E-05 1.5401840E-03 at 50iterations finished qdiffx linear iterations at : 21:15:23 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.1401637E-05 1.5401840E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 21:15:24 3.365u 0.201s 0:03.85 92.4% 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 21:15:24 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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: ZN4 492 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.887593 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): -31.62100 17.49900 ymin,ymax (A): -23.63100 22.66200 zmin,zma (A): -12.44700 44.13300 x,y,z range (A): 49.12000 46.29300 56.58000 scale (grids/A): 1.887593 object centre (A): -7.061000 -0.4845009 15.84300 number of atom coordinates read : 2594 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 392.2440 centred at (gu) : 85.54546 87.96888 89.71869 assigned negative charge : -388.3386 centred at (gu) : 85.28121 88.10756 89.35614 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 72334 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21236 grid for indexing accessible points = 1.400000 m= 24965 mr = 50926 m= 3474 mr = 18426 m= 168 mr = 2114 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 5347 time to turn everything in is 0.5100000 number of dielectric boundary points 29436 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 143 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 19258 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) : 0.6291976 object centre at (A) : -7.061000 -0.4845009 15.84300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1464290E-02 3.3589948E-02 midg,1,midg; midg,igrid,midg 1.4446309E-02 2.3410846E-03 1,midg,midg; igrid,midg,midg -3.8076059E-03 3.1424254E-02 gauss-seidel spectral radius is 0.9986022 estimated iterations to convergence 212 setup time was (sec) 0.8000000 now iterating at: 21:15:25 rms-change max change #iterations 4.133043 154.9031 at 10iterations 1.922288 62.79480 at 20iterations 0.8902527 28.22266 at 30iterations 0.4137933 14.46943 at 40iterations 0.1923029 5.968723 at 50iterations 8.9323930E-02 2.880074 at 60iterations 4.1395694E-02 1.308382 at 70iterations 1.9296246E-02 0.6394100 at 80iterations 8.9426832E-03 0.2760544 at 90iterations 4.1461694E-03 0.1313324 at 100iterations 1.9315589E-03 6.6024780E-02 at 110iterations 8.9813670E-04 2.9757500E-02 at 120iterations finished qdiffx linear iterations at : 21:15:32 total time elapsed so far: 7.360000 # loops : 120 mean,max change (kT/e) : 8.9813670E-04 2.9757500E-02 energy calculations done at 7.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.540000 DelPhi exited at 21:15:32 7.539u 0.228s 0:08.07 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 Sat Oct 8 2011 at 21:15:32 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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: ZN4 492 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.831389 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): -31.62100 17.49900 ymin,ymax (A): -23.63100 22.66200 zmin,zma (A): -12.44700 44.13300 x,y,z range (A): 49.12000 46.29300 56.58000 scale (grids/A): 2.831389 object centre (A): -7.061000 -0.4845009 15.84300 number of atom coordinates read : 2594 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 392.2440 centred at (gu) : 83.31801 86.95314 89.57777 assigned negative charge : -388.3386 centred at (gu) : 82.92182 87.16146 89.03416 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 167470 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21236 grid for indexing accessible points = 1.400000 m= 83210 mr = 123056 m= 27870 mr = 68787 m= 6105 mr = 22193 m= 763 mr = 4543 m= 44 mr = 470 m= 0 mr = 19 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 17839 time to turn everything in is 1.280000 number of dielectric boundary points 66394 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 19600 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) : 1.887593 object centre at (A) : -7.061000 -0.4845009 15.84300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1655561 0.4903548 midg,1,midg; midg,igrid,midg 0.1678012 2.5023354E-02 1,midg,midg; igrid,midg,midg -8.8654868E-03 0.4185026 gauss-seidel spectral radius is 0.9992417 estimated iterations to convergence 287 setup time was (sec) 1.590000 now iterating at: 21:15:34 rms-change max change #iterations 9.663876 377.3257 at 10iterations 5.564968 129.6301 at 20iterations 3.185735 66.44328 at 30iterations 1.819248 34.37076 at 40iterations 1.041105 19.46989 at 50iterations 0.5934597 11.75994 at 60iterations 0.3386281 5.969116 at 70iterations 0.1939768 3.687490 at 80iterations 0.1102746 2.016625 at 90iterations 6.2889062E-02 1.177559 at 100iterations 3.5977945E-02 0.8605270 at 110iterations 2.0495409E-02 0.3775539 at 120iterations 1.1694486E-02 0.2307286 at 130iterations 6.6730599E-03 0.1277809 at 140iterations 3.7993821E-03 7.7171326E-02 at 150iterations 2.1656095E-03 3.6268473E-02 at 160iterations 1.2367469E-03 2.2737980E-02 at 170iterations 7.0710771E-04 1.4560699E-02 at 180iterations finished qdiffx linear iterations at : 21:15:44 total time elapsed so far: 12.01000 # loops : 180 mean,max change (kT/e) : 7.0710771E-04 1.4560699E-02 energy calculations done at 12.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.20000 DelPhi exited at 21:15:45 12.199u 0.231s 0:12.70 97.7% 0+0k 0+0io 0pf+0w