Thu Jan 19 11:44:50 PST 2012 #!/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 Thu Jan 19 2012 at 11:44:54 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5069 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: 0.4914480 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): -28.56900 35.18400 ymin,ymax (A): -36.60100 35.83800 zmin,zma (A): -9.051000 58.70600 x,y,z range (A): 63.75300 72.43900 67.75700 scale (grids/A): 0.4914480 object centre (A): 3.307501 -0.3815022 24.82750 number of atom coordinates read : 5069 total number of charged atoms : 4904 net assigned charge : -3.999959 assigned positive charge : 766.5165 centred at (gu) : 90.05512 90.29095 91.25862 assigned negative charge : -770.5209 centred at (gu) : 89.97276 90.32175 91.21035 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8101 nv = 96 ne = 84 npr = 95441 no. pairs analyzed = 95441 no. exposed pairs = 7122 no. arc points = 51121 no. surface atoms = 2359 nbur = 2710 mkacc time = 0.1700000 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 = 1.736000 m= 259 mr = 3766 m= 0 mr = 1 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 4593 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4856 ## 802 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 10852 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8299365E-11 4.7671578E-11 midg,1,midg; midg,igrid,midg 1.1528524E-11 -6.6050720E-11 1,midg,midg; igrid,midg,midg -1.2168536E-10 7.4323214E-11 gauss-seidel spectral radius is 0.9788812 estimated iterations to convergence 57 setup time was (sec) 0.5200000 now iterating at: 11:44:58 rms-change max change #iterations 5.4750722E-02 11.09883 at 10iterations 3.2281990E-03 0.5088043 at 20iterations 5.8244698E-04 5.9989929E-02 at 30iterations 2.0054373E-04 1.7496109E-02 at 40iterations 7.0821858E-05 6.1531067E-03 at 50iterations finished qdiffx linear iterations at : 11:45:08 total time elapsed so far: 3.580000 # loops : 50 mean,max change (kT/e) : 7.0821858E-05 6.1531067E-03 energy calculations done at 3.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.710000 DelPhi exited at 11:45:10 3.711u 0.191s 0:15.89 24.5% 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 Thu Jan 19 2012 at 11:45:12 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5069 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: 1.474344 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): -28.56900 35.18400 ymin,ymax (A): -36.60100 35.83800 zmin,zma (A): -9.051000 58.70600 x,y,z range (A): 63.75300 72.43900 67.75700 scale (grids/A): 1.474344 object centre (A): 3.307501 -0.3815022 24.82750 number of atom coordinates read : 5069 total number of charged atoms : 4904 net assigned charge : -3.999959 assigned positive charge : 766.5165 centred at (gu) : 90.16391 90.87122 93.77466 assigned negative charge : -770.5209 centred at (gu) : 89.91781 90.96484 93.63023 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 91353 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51121 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 23951 mr = 59163 m= 1676 mr = 14670 m= 21 mr = 428 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 718 time to turn everything in is 0.4500000 number of dielectric boundary points 42740 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 690 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 36307 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) : 0.4914480 object centre at (A) : 3.307501 -0.3815022 24.82750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.7096329E-03 -8.4104575E-03 midg,1,midg; midg,igrid,midg 9.7437501E-03 -1.5317540E-02 1,midg,midg; igrid,midg,midg -1.0528290E-03 6.9300686E-03 gauss-seidel spectral radius is 0.9980091 estimated iterations to convergence 178 setup time was (sec) 0.6800000 now iterating at: 11:45:17 rms-change max change #iterations 3.636289 159.1702 at 10iterations 1.450068 54.57413 at 20iterations 0.5800707 19.54021 at 30iterations 0.2326664 7.435659 at 40iterations 9.3241408E-02 3.118134 at 50iterations 3.7356906E-02 1.181308 at 60iterations 1.5058934E-02 0.4851990 at 70iterations 6.0638888E-03 0.1917725 at 80iterations 2.4910537E-03 8.6383820E-02 at 90iterations 1.0592694E-03 3.3899307E-02 at 100iterations 4.8427860E-04 1.4942169E-02 at 110iterations 2.4831816E-04 7.1868896E-03 at 120iterations finished qdiffx linear iterations at : 11:45:39 total time elapsed so far: 8.150000 # loops : 120 mean,max change (kT/e) : 2.4831816E-04 7.1868896E-03 energy calculations done at 8.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.280000 DelPhi exited at 11:45:40 8.283u 0.216s 0:29.60 28.6% 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 Thu Jan 19 2012 at 11:45:43 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5069 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: 2.211516 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): -28.56900 35.18400 ymin,ymax (A): -36.60100 35.83800 zmin,zma (A): -9.051000 58.70600 x,y,z range (A): 63.75300 72.43900 67.75700 scale (grids/A): 2.211516 object centre (A): 3.307501 -0.3815022 24.82750 number of atom coordinates read : 5069 total number of charged atoms : 4904 net assigned charge : -3.999959 assigned positive charge : 766.5165 centred at (gu) : 90.24545 91.30651 95.66158 assigned negative charge : -770.5209 centred at (gu) : 89.87659 91.44711 95.44530 start vw surface at 0.1200000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 213337 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51121 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 88870 mr = 147229 m= 19342 mr = 66138 m= 1978 mr = 12673 m= 61 mr = 834 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 2232 time to turn everything in is 1.070000 number of dielectric boundary points 96703 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 39082 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) : 1.474344 object centre at (A) : 3.307501 -0.3815022 24.82750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7848970E-02 -0.1449931 midg,1,midg; midg,igrid,midg 0.2285459 -0.2370324 1,midg,midg; igrid,midg,midg 1.0298835E-02 0.1242349 gauss-seidel spectral radius is 0.9991571 estimated iterations to convergence 272 setup time was (sec) 1.330000 now iterating at: 11:45:50 rms-change max change #iterations 10.24113 302.5566 at 10iterations 5.875706 155.1668 at 20iterations 3.353570 80.50983 at 30iterations 1.898643 42.17832 at 40iterations 1.073363 22.25703 at 50iterations 0.6043823 14.70747 at 60iterations 0.3386717 7.371525 at 70iterations 0.1898526 4.126762 at 80iterations 0.1062850 2.147964 at 90iterations 5.9235480E-02 1.106064 at 100iterations 3.3065923E-02 0.7517548 at 110iterations 1.8416936E-02 0.3806057 at 120iterations 1.0213782E-02 0.2200394 at 130iterations 5.6932033E-03 0.1244221 at 140iterations 3.1675124E-03 6.4697266E-02 at 150iterations 1.7617629E-03 3.3447266E-02 at 160iterations 9.7630755E-04 1.9075871E-02 at 170iterations 5.4478989E-04 1.1032104E-02 at 180iterations finished qdiffx linear iterations at : 11:46:27 total time elapsed so far: 13.64000 # loops : 180 mean,max change (kT/e) : 5.4478989E-04 1.1032104E-02 energy calculations done at 13.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.77000 DelPhi exited at 11:46:28 13.771u 0.224s 0:46.32 30.2% 0+0k 0+0io 0pf+0w