Tue Oct 11 03:19:46 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 Tue Oct 11 2011 at 03:19:46 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3185 !!! WARNING: GLM 12 has a net charge of -0.0940 !!! WARNING: SEP 223 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5375126 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): -3.755000 46.19200 ymin,ymax (A): 70.83600 137.0670 zmin,zma (A): 102.6280 162.2500 x,y,z range (A): 49.94700 66.23100 59.62200 scale (grids/A): 0.5375126 object centre (A): 21.21850 103.9515 132.4390 number of atom coordinates read : 3185 total number of charged atoms : 3040 net assigned charge : -6.568974 assigned positive charge : 477.8208 centred at (gu) : 91.07629 92.94500 91.40039 assigned negative charge : -484.3909 centred at (gu) : 91.03458 92.97075 91.39387 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5740 nv = 96 ne = 84 npr = 66439 no. pairs analyzed = 66439 no. exposed pairs = 3857 no. arc points = 27002 no. surface atoms = 1301 nbur = 1884 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 248 mr = 3035 m= 0 mr = 6 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 2947 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2719 ## 374 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7724 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2788237E-10 -3.5564007E-10 midg,1,midg; midg,igrid,midg -7.8143741E-11 -8.8136604E-10 1,midg,midg; igrid,midg,midg -3.8565209E-10 -9.0173674E-11 gauss-seidel spectral radius is 0.9821703 estimated iterations to convergence 62 setup time was (sec) 0.4200000 now iterating at: 03:19:47 rms-change max change #iterations 7.3708646E-02 11.09236 at 10iterations 4.7895354E-03 0.8453579 at 20iterations 3.9394404E-04 6.8950653E-02 at 30iterations 5.6438854E-05 1.0450661E-02 at 40iterations 1.1427323E-05 2.3044012E-03 at 50iterations finished qdiffx linear iterations at : 03:19:50 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 1.1427323E-05 2.3044012E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 03:19:50 3.458u 0.171s 0:04.08 88.7% 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 Tue Oct 11 2011 at 03:19:50 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3185 !!! WARNING: GLM 12 has a net charge of -0.0940 !!! WARNING: SEP 223 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.612538 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): -3.755000 46.19200 ymin,ymax (A): 70.83600 137.0670 zmin,zma (A): 102.6280 162.2500 x,y,z range (A): 49.94700 66.23100 59.62200 scale (grids/A): 1.612538 object centre (A): 21.21850 103.9515 132.4390 number of atom coordinates read : 3185 total number of charged atoms : 3040 net assigned charge : -6.568974 assigned positive charge : 477.8208 centred at (gu) : 93.22797 98.83427 94.20036 assigned negative charge : -484.3909 centred at (gu) : 93.10339 98.91190 94.18102 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 64161 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27002 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 19530 mr = 43682 m= 1927 mr = 13585 m= 46 mr = 928 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 380 time to turn everything in is 0.3400000 number of dielectric boundary points 27465 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 362 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 23237 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) : 0.5375126 object centre at (A) : 21.21850 103.9515 132.4390 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2249910E-03 5.1530027E-03 midg,1,midg; midg,igrid,midg 2.6958909E-02 -1.3927297E-02 1,midg,midg; igrid,midg,midg -7.3146704E-03 -4.2766379E-03 gauss-seidel spectral radius is 0.9981417 estimated iterations to convergence 184 setup time was (sec) 0.5600000 now iterating at: 03:19:51 rms-change max change #iterations 3.357139 156.0938 at 10iterations 1.378831 56.71624 at 20iterations 0.5703269 24.08842 at 30iterations 0.2353062 8.514341 at 40iterations 9.7298317E-02 3.271177 at 50iterations 4.0079609E-02 1.394910 at 60iterations 1.6600361E-02 0.5744324 at 70iterations 6.8861120E-03 0.2523766 at 80iterations 2.8698808E-03 0.1086144 at 90iterations 1.1941550E-03 4.6562195E-02 at 100iterations 5.0676486E-04 2.0526409E-02 at 110iterations 2.1934594E-04 9.4909668E-03 at 120iterations finished qdiffx linear iterations at : 03:19:58 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 2.1934594E-04 9.4909668E-03 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 03:19:59 7.754u 0.196s 0:08.29 95.7% 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 Tue Oct 11 2011 at 03:19:59 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3185 !!! WARNING: GLM 12 has a net charge of -0.0940 !!! WARNING: SEP 223 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.418807 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): -3.755000 46.19200 ymin,ymax (A): 70.83600 137.0670 zmin,zma (A): 102.6280 162.2500 x,y,z range (A): 49.94700 66.23100 59.62200 scale (grids/A): 2.418807 object centre (A): 21.21850 103.9515 132.4390 number of atom coordinates read : 3185 total number of charged atoms : 3040 net assigned charge : -6.568974 assigned positive charge : 477.8208 centred at (gu) : 94.84181 103.2510 96.30045 assigned negative charge : -484.3909 centred at (gu) : 94.65513 103.3677 96.27147 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 149048 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27002 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 67865 mr = 106671 m= 18986 mr = 54024 m= 2976 mr = 14450 m= 175 mr = 1963 m= 3 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 1288 time to turn everything in is 0.7800000 number of dielectric boundary points 61860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 24275 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) : 1.612538 object centre at (A) : 21.21850 103.9515 132.4390 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0856765E-03 0.1898939 midg,1,midg; midg,igrid,midg 0.5024973 -0.3536680 1,midg,midg; igrid,midg,midg -0.1051051 -5.6145765E-02 gauss-seidel spectral radius is 0.9991235 estimated iterations to convergence 267 setup time was (sec) 1.020000 now iterating at: 03:20:00 rms-change max change #iterations 8.792390 266.3457 at 10iterations 4.885602 131.9454 at 20iterations 2.710350 72.94006 at 30iterations 1.495609 32.56588 at 40iterations 0.8222975 19.19545 at 50iterations 0.4528689 9.979636 at 60iterations 0.2480611 5.075416 at 70iterations 0.1363517 2.870790 at 80iterations 7.4599534E-02 1.645292 at 90iterations 4.0807720E-02 0.8977604 at 100iterations 2.2305144E-02 0.5009809 at 110iterations 1.2203665E-02 0.2691765 at 120iterations 6.7149531E-03 0.1406021 at 130iterations 3.6764697E-03 7.7090502E-02 at 140iterations 2.0165530E-03 4.4013977E-02 at 150iterations 1.1114586E-03 2.1683693E-02 at 160iterations 6.1812508E-04 1.2850761E-02 at 170iterations 3.4722275E-04 7.2250366E-03 at 180iterations finished qdiffx linear iterations at : 03:20:11 total time elapsed so far: 12.27000 # loops : 180 mean,max change (kT/e) : 3.4722275E-04 7.2250366E-03 energy calculations done at 12.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.40000 DelPhi exited at 03:20:12 12.407u 0.207s 0:12.99 96.9% 0+0k 0+0io 0pf+0w