Wed Dec 21 14:20:58 PST 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 Wed Dec 21 2011 at 14:20:59 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5914015 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): -35.34000 9.910000 ymin,ymax (A): 1.426000 41.09300 zmin,zma (A): -1.968000 58.22800 x,y,z range (A): 45.25000 39.66700 60.19600 scale (grids/A): 0.5914015 object centre (A): -12.71500 21.25950 28.13000 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000005 assigned positive charge : 290.5001 centred at (gu) : 90.52536 89.53945 89.75845 assigned negative charge : -288.5003 centred at (gu) : 90.43728 89.68041 89.74609 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4643 nv = 96 ne = 84 npr = 40466 no. pairs analyzed = 40466 no. exposed pairs = 2440 no. arc points = 17052 no. surface atoms = 827 nbur = 1143 mkacc time = 7.0000008E-02 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 = 1.456000 m= 185 mr = 2550 m= 0 mr = 23 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2255 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1739 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 5647 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8605771E-10 8.3200880E-10 midg,1,midg; midg,igrid,midg 3.8898835E-09 -2.1025020E-09 1,midg,midg; igrid,midg,midg -1.0756297E-09 2.7430564E-09 gauss-seidel spectral radius is 0.9851536 estimated iterations to convergence 67 setup time was (sec) 0.3500000 now iterating at: 14:20:59 rms-change max change #iterations 8.4710553E-02 13.95894 at 10iterations 6.8753487E-03 1.308443 at 20iterations 5.5909832E-04 0.1017553 at 30iterations 4.5309156E-05 8.2201958E-03 at 40iterations 3.6946637E-06 7.3623657E-04 at 50iterations finished qdiffx linear iterations at : 14:21:03 total time elapsed so far: 3.950000 # loops : 50 mean,max change (kT/e) : 3.6946637E-06 7.3623657E-04 energy calculations done at 3.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.090000 DelPhi exited at 14:21:04 4.092u 0.226s 0:05.28 81.6% 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 Wed Dec 21 2011 at 14:21:04 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.774204 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): -35.34000 9.910000 ymin,ymax (A): 1.426000 41.09300 zmin,zma (A): -1.968000 58.22800 x,y,z range (A): 45.25000 39.66700 60.19600 scale (grids/A): 1.774204 object centre (A): -12.71500 21.25950 28.13000 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000005 assigned positive charge : 290.5001 centred at (gu) : 91.57639 88.61848 89.27546 assigned negative charge : -288.5003 centred at (gu) : 91.31199 89.04162 89.23846 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 50237 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17052 grid for indexing accessible points = 1.400000 m= 17782 mr = 34495 m= 2194 mr = 13417 m= 84 mr = 1365 m= 0 mr = 25 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 843 time to turn everything in is 0.3000000 number of dielectric boundary points 20995 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 14278 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) : 0.5914015 object centre at (A) : -12.71500 21.25950 28.13000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8839279E-02 2.2678094E-02 midg,1,midg; midg,igrid,midg 1.1528034E-03 -9.8479418E-03 1,midg,midg; igrid,midg,midg -3.4844398E-03 -1.1269578E-03 gauss-seidel spectral radius is 0.9983500 estimated iterations to convergence 195 setup time was (sec) 0.5900000 now iterating at: 14:21:05 rms-change max change #iterations 3.092093 167.3706 at 10iterations 1.342812 64.51845 at 20iterations 0.5861250 21.90774 at 30iterations 0.2530442 9.831802 at 40iterations 0.1092440 4.453901 at 50iterations 4.7619559E-02 1.877428 at 60iterations 2.0712722E-02 0.7950172 at 70iterations 8.9735370E-03 0.3339815 at 80iterations 3.9067906E-03 0.1609497 at 90iterations 1.6941988E-03 6.3461304E-02 at 100iterations 7.3466246E-04 2.6752472E-02 at 110iterations 3.1944792E-04 1.1717796E-02 at 120iterations finished qdiffx linear iterations at : 14:21:16 total time elapsed so far: 11.87000 # loops : 120 mean,max change (kT/e) : 3.1944792E-04 1.1717796E-02 energy calculations done at 11.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.01000 DelPhi exited at 14:21:20 12.009u 0.461s 0:16.32 76.3% 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 Wed Dec 21 2011 at 14:21:22 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 = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.661306 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): -35.34000 9.910000 ymin,ymax (A): 1.426000 41.09300 zmin,zma (A): -1.968000 58.22800 x,y,z range (A): 45.25000 39.66700 60.19600 scale (grids/A): 2.661306 object centre (A): -12.71500 21.25950 28.13000 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000005 assigned positive charge : 290.5001 centred at (gu) : 92.36460 87.92768 88.91320 assigned negative charge : -288.5003 centred at (gu) : 91.96798 88.56247 88.85777 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 115973 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17052 grid for indexing accessible points = 1.400000 m= 58766 mr = 83264 m= 19839 mr = 48768 m= 3812 mr = 16310 m= 420 mr = 2880 m= 6 mr = 287 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 2912 time to turn everything in is 0.6500000 number of dielectric boundary points 47307 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 14701 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) : 1.774204 object centre at (A) : -12.71500 21.25950 28.13000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2935082 0.1801210 midg,1,midg; midg,igrid,midg -1.7173644E-02 -0.1293192 1,midg,midg; igrid,midg,midg -6.0534380E-02 -5.9155647E-02 gauss-seidel spectral radius is 0.9991567 estimated iterations to convergence 272 setup time was (sec) 0.8900000 now iterating at: 14:21:25 rms-change max change #iterations 7.503346 262.2424 at 10iterations 4.196127 154.4562 at 20iterations 2.339413 59.41526 at 30iterations 1.296736 30.35124 at 40iterations 0.7192311 16.43685 at 50iterations 0.3985927 9.557175 at 60iterations 0.2204014 5.395821 at 70iterations 0.1219895 2.727692 at 80iterations 6.7222171E-02 1.454198 at 90iterations 3.7249073E-02 0.8805075 at 100iterations 2.0589948E-02 0.4736938 at 110iterations 1.1351711E-02 0.2451916 at 120iterations 6.2750587E-03 0.1372070 at 130iterations 3.4600284E-03 8.6696148E-02 at 140iterations 1.9133143E-03 4.2618752E-02 at 150iterations 1.0551065E-03 2.3633957E-02 at 160iterations 5.8393908E-04 1.2848854E-02 at 170iterations 3.2204267E-04 7.2069168E-03 at 180iterations finished qdiffx linear iterations at : 14:21:39 total time elapsed so far: 14.99000 # loops : 180 mean,max change (kT/e) : 3.2204267E-04 7.2069168E-03 energy calculations done at 14.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.12000 DelPhi exited at 14:21:43 15.126u 0.279s 0:20.93 73.5% 0+0k 0+0io 0pf+0w