Sat Oct 8 21:28:43 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 Sat Oct 8 2011 at 21:28:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2622 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: 0.6455356 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): -28.29000 23.79200 ymin,ymax (A): -27.18000 27.96800 zmin,zma (A): -8.199000 42.62900 x,y,z range (A): 52.08200 55.14800 50.82800 scale (grids/A): 0.6455356 object centre (A): -2.249000 0.3940001 17.21500 number of atom coordinates read : 2622 total number of charged atoms : 2486 net assigned charge : 3.500005 assigned positive charge : 394.3248 centred at (gu) : 92.94063 90.37937 92.49174 assigned negative charge : -390.8253 centred at (gu) : 92.90626 90.37711 92.48438 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7492 nv = 96 ne = 84 npr = 52025 no. pairs analyzed = 52025 no. exposed pairs = 3449 no. arc points = 24487 no. surface atoms = 1146 nbur = 1476 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 430 mr = 4024 m= 3 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2275 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8832 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8619089E-09 1.1236798E-08 midg,1,midg; midg,igrid,midg 4.9834292E-09 6.4731220E-09 1,midg,midg; igrid,midg,midg 6.7459333E-10 1.9259298E-08 gauss-seidel spectral radius is 0.9875720 estimated iterations to convergence 73 setup time was (sec) 0.4000000 now iterating at: 21:28:44 rms-change max change #iterations 0.1528499 20.77261 at 10iterations 1.5226982E-02 2.334554 at 20iterations 1.5574082E-03 0.2084646 at 30iterations 1.8081658E-04 2.1020889E-02 at 40iterations 3.4267046E-05 4.2686462E-03 at 50iterations finished qdiffx linear iterations at : 21:28:47 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 3.4267046E-05 4.2686462E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 21:28:47 3.416u 0.171s 0:03.88 92.2% 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 21:28:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2622 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.936607 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): -28.29000 23.79200 ymin,ymax (A): -27.18000 27.96800 zmin,zma (A): -8.199000 42.62900 x,y,z range (A): 52.08200 55.14800 50.82800 scale (grids/A): 1.936607 object centre (A): -2.249000 0.3940001 17.21500 number of atom coordinates read : 2622 total number of charged atoms : 2486 net assigned charge : 3.500005 assigned positive charge : 394.3248 centred at (gu) : 98.82127 91.13748 97.47470 assigned negative charge : -390.8253 centred at (gu) : 98.71825 91.13116 97.45276 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 80522 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24487 grid for indexing accessible points = 1.400000 m= 28832 mr = 55614 m= 4608 mr = 20459 m= 287 mr = 2739 m= 7 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 366 time to turn everything in is 0.3800000 number of dielectric boundary points 35347 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 19555 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) : 0.6455356 object centre at (A) : -2.249000 0.3940001 17.21500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4785332E-02 -3.5145576E-03 midg,1,midg; midg,igrid,midg 1.8040393E-02 -3.4734644E-02 1,midg,midg; igrid,midg,midg 2.2753661E-02 4.8699668E-03 gauss-seidel spectral radius is 0.9986805 estimated iterations to convergence 218 setup time was (sec) 0.6000000 now iterating at: 21:28:48 rms-change max change #iterations 4.422710 195.5226 at 10iterations 2.097617 76.90456 at 20iterations 0.9980626 35.53247 at 30iterations 0.4735864 16.78457 at 40iterations 0.2246798 7.342459 at 50iterations 0.1069041 3.283821 at 60iterations 5.0734203E-02 1.525872 at 70iterations 2.4090610E-02 0.7143354 at 80iterations 1.1432539E-02 0.3907585 at 90iterations 5.4309135E-03 0.1726418 at 100iterations 2.5862260E-03 7.8523874E-02 at 110iterations 1.2287297E-03 3.4301758E-02 at 120iterations finished qdiffx linear iterations at : 21:28:55 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 1.2287297E-03 3.4301758E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 21:28:56 7.763u 0.215s 0:08.31 95.9% 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 Sat Oct 8 2011 at 21:28:56 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2622 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.904910 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): -28.29000 23.79200 ymin,ymax (A): -27.18000 27.96800 zmin,zma (A): -8.199000 42.62900 x,y,z range (A): 52.08200 55.14800 50.82800 scale (grids/A): 2.904910 object centre (A): -2.249000 0.3940001 17.21500 number of atom coordinates read : 2622 total number of charged atoms : 2486 net assigned charge : 3.500005 assigned positive charge : 394.3248 centred at (gu) : 103.2317 91.70605 101.2118 assigned negative charge : -390.8253 centred at (gu) : 103.0773 91.69665 101.1789 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 186405 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24487 grid for indexing accessible points = 1.400000 m= 93853 mr = 134900 m= 33176 mr = 75789 m= 8298 mr = 25686 m= 1194 mr = 5992 m= 59 mr = 726 m= 3 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 1201 time to turn everything in is 1.020000 number of dielectric boundary points 79877 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 19883 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) : 1.936607 object centre at (A) : -2.249000 0.3940001 17.21500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1772287 -3.8807511E-02 midg,1,midg; midg,igrid,midg 7.7767484E-02 -1.106710 1,midg,midg; igrid,midg,midg 0.2064730 -6.1440233E-02 gauss-seidel spectral radius is 0.9992821 estimated iterations to convergence 294 setup time was (sec) 1.260000 now iterating at: 21:28:57 rms-change max change #iterations 10.41654 319.7052 at 10iterations 6.205365 162.0985 at 20iterations 3.666167 87.41048 at 30iterations 2.162683 43.57005 at 40iterations 1.271663 29.08195 at 50iterations 0.7420189 14.58179 at 60iterations 0.4345607 9.065338 at 70iterations 0.2535326 4.768932 at 80iterations 0.1475876 2.734966 at 90iterations 8.5887603E-02 1.584845 at 100iterations 4.9922440E-02 0.8888264 at 110iterations 2.9061781E-02 0.4867783 at 120iterations 1.6877260E-02 0.3069286 at 130iterations 9.8119834E-03 0.1657705 at 140iterations 5.6935283E-03 0.1071415 at 150iterations 3.3060240E-03 5.9267044E-02 at 160iterations 1.9188302E-03 3.5824776E-02 at 170iterations 1.1149033E-03 2.1244049E-02 at 180iterations finished qdiffx linear iterations at : 21:29:09 total time elapsed so far: 12.70000 # loops : 180 mean,max change (kT/e) : 1.1149033E-03 2.1244049E-02 energy calculations done at 12.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.83000 DelPhi exited at 21:29:09 12.832u 0.212s 0:13.31 97.9% 0+0k 0+0io 0pf+0w