Sat Oct 8 15:48:24 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 15:48:24 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2377 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 0.6421125 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): -1.990000 47.45200 ymin,ymax (A): -17.46700 30.28700 zmin,zma (A): -19.12500 36.31700 x,y,z range (A): 49.44200 47.75400 55.44200 scale (grids/A): 0.6421125 object centre (A): 22.73100 6.409999 8.595999 number of atom coordinates read : 2377 total number of charged atoms : 2308 net assigned charge : 6.806004 assigned positive charge : 356.7340 centred at (gu) : 90.51564 89.08336 90.30682 assigned negative charge : -349.9288 centred at (gu) : 90.47128 89.18118 90.30231 start vw surface at 0.1500000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6889 nv = 96 ne = 84 npr = 46015 no. pairs analyzed = 46015 no. exposed pairs = 3192 no. arc points = 22257 no. surface atoms = 1074 nbur = 1303 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 364 mr = 3702 m= 3 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3495 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2175 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8086 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.2773869E-09 1.1593267E-08 midg,1,midg; midg,igrid,midg 2.5716467E-08 -4.2049664E-10 1,midg,midg; igrid,midg,midg 4.9017341E-09 1.7045947E-08 gauss-seidel spectral radius is 0.9874206 estimated iterations to convergence 73 setup time was (sec) 0.7000000 now iterating at: 15:48:25 rms-change max change #iterations 0.1388189 19.94117 at 10iterations 1.3912266E-02 1.993765 at 20iterations 1.4866829E-03 0.2164345 at 30iterations 2.3778462E-04 3.4152985E-02 at 40iterations 6.5320193E-05 9.8199844E-03 at 50iterations finished qdiffx linear iterations at : 15:48:28 total time elapsed so far: 4.350000 # loops : 50 mean,max change (kT/e) : 6.5320193E-05 9.8199844E-03 energy calculations done at 4.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.570000 DelPhi exited at 15:48:29 4.575u 0.403s 0:05.31 93.5% 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 15:48:29 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2377 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 1.926337 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): -1.990000 47.45200 ymin,ymax (A): -17.46700 30.28700 zmin,zma (A): -19.12500 36.31700 x,y,z range (A): 49.44200 47.75400 55.44200 scale (grids/A): 1.926337 object centre (A): 22.73100 6.409999 8.595999 number of atom coordinates read : 2377 total number of charged atoms : 2308 net assigned charge : 6.806004 assigned positive charge : 356.7340 centred at (gu) : 91.54656 87.24947 90.91982 assigned negative charge : -349.9288 centred at (gu) : 91.41370 87.54345 90.90677 start vw surface at 0.1400000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 73316 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22257 grid for indexing accessible points = 1.400000 m= 27591 mr = 50563 m= 5270 mr = 20151 m= 379 mr = 3521 m= 5 mr = 156 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7500000 number of dielectric boundary points 32170 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 18180 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) : 0.6421125 object centre at (A) : 22.73100 6.409999 8.595999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3363614E-02 -1.0780876E-02 midg,1,midg; midg,igrid,midg 2.6079297E-02 -2.9572290E-03 1,midg,midg; igrid,midg,midg 1.1635548E-02 -1.3345412E-02 gauss-seidel spectral radius is 0.9986541 estimated iterations to convergence 216 setup time was (sec) 1.080000 now iterating at: 15:48:30 rms-change max change #iterations 4.140305 160.8487 at 10iterations 1.945980 88.85007 at 20iterations 0.9137580 33.94294 at 30iterations 0.4321863 13.89608 at 40iterations 0.2035116 6.193230 at 50iterations 9.5765084E-02 3.256429 at 60iterations 4.5129791E-02 1.391079 at 70iterations 2.1243695E-02 0.6386871 at 80iterations 1.0040826E-02 0.3110695 at 90iterations 4.7652773E-03 0.1464958 at 100iterations 2.2644545E-03 7.5107574E-02 at 110iterations 1.0901506E-03 3.3786774E-02 at 120iterations finished qdiffx linear iterations at : 15:48:40 total time elapsed so far: 10.29000 # loops : 120 mean,max change (kT/e) : 1.0901506E-03 3.3786774E-02 energy calculations done at 10.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.51000 DelPhi exited at 15:48:40 10.517u 0.449s 0:11.28 97.0% 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 15:48:40 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2377 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 2.889506 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): -1.990000 47.45200 ymin,ymax (A): -17.46700 30.28700 zmin,zma (A): -19.12500 36.31700 x,y,z range (A): 49.44200 47.75400 55.44200 scale (grids/A): 2.889506 object centre (A): 22.73100 6.409999 8.595999 number of atom coordinates read : 2377 total number of charged atoms : 2308 net assigned charge : 6.806004 assigned positive charge : 356.7340 centred at (gu) : 92.31977 85.87411 91.37955 assigned negative charge : -349.9288 centred at (gu) : 92.12061 86.31503 91.36014 start vw surface at 0.1600000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 169506 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22257 grid for indexing accessible points = 1.400000 m= 86938 mr = 122536 m= 34275 mr = 70539 m= 9870 mr = 27702 m= 1732 mr = 7782 m= 104 mr = 1257 m= 1 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.000000 number of dielectric boundary points 72547 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.170000 number of grid points assigned charge 18463 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) : 1.926337 object centre at (A) : 22.73100 6.409999 8.595999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2724507 -0.2138421 midg,1,midg; midg,igrid,midg 0.1939453 -7.8995876E-02 1,midg,midg; igrid,midg,midg 9.9489346E-02 -0.3796218 gauss-seidel spectral radius is 0.9992667 estimated iterations to convergence 291 setup time was (sec) 2.390000 now iterating at: 15:48:43 rms-change max change #iterations 9.796646 359.0670 at 10iterations 5.802526 130.9905 at 20iterations 3.414279 71.02985 at 30iterations 1.999811 39.35821 at 40iterations 1.167706 23.91223 at 50iterations 0.6817093 12.25269 at 60iterations 0.3961815 7.226240 at 70iterations 0.2297160 4.271626 at 80iterations 0.1331761 2.513442 at 90iterations 7.7318251E-02 1.455100 at 100iterations 4.4734847E-02 0.8820686 at 110iterations 2.5850564E-02 0.4934845 at 120iterations 1.4950923E-02 0.2584808 at 130iterations 8.6298613E-03 0.1648111 at 140iterations 4.9740337E-03 9.8447800E-02 at 150iterations 2.8752538E-03 5.1397324E-02 at 160iterations 1.6598380E-03 2.9823303E-02 at 170iterations 9.5591403E-04 1.6536713E-02 at 180iterations finished qdiffx linear iterations at : 15:48:59 total time elapsed so far: 17.96000 # loops : 180 mean,max change (kT/e) : 9.5591403E-04 1.6536713E-02 energy calculations done at 17.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.17000 DelPhi exited at 15:48:59 18.172u 0.470s 0:18.93 98.4% 0+0k 0+0io 0pf+0w