Mon Oct 10 14:16:12 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 Mon Oct 10 2011 at 14:16:12 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2160 !!! WARNING: SEP 119 has a net charge of -0.4750 !!! WARNING: GLM 120 has a net charge of -0.0940 !!! WARNING: HIT 142 has a net charge of 0.5140 !!! WARNING: MG3 318 has a net charge of 1.4000 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: 0.7358260 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): 15.05800 54.48400 ymin,ymax (A): -7.529000 40.85200 zmin,zma (A): -5.098000 38.51800 x,y,z range (A): 39.42599 48.38100 43.61600 scale (grids/A): 0.7358260 object centre (A): 34.77100 16.66150 16.71000 number of atom coordinates read : 2160 total number of charged atoms : 2022 net assigned charge : -3.154987 assigned positive charge : 325.9306 centred at (gu) : 89.13049 90.54974 89.11660 assigned negative charge : -329.0859 centred at (gu) : 89.14619 90.52979 89.11600 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7718 nv = 96 ne = 84 npr = 46219 no. pairs analyzed = 46219 no. exposed pairs = 2484 no. arc points = 16721 no. surface atoms = 850 nbur = 1310 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 582 mr = 4630 m= 2 mr = 138 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 212 time to turn everything in is 0.1700000 number of dielectric boundary points 3534 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1405 ## 104 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8603 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.0533480E-08 -4.2983633E-08 midg,1,midg; midg,igrid,midg -6.3375488E-08 -3.5098719E-08 1,midg,midg; igrid,midg,midg -4.1934502E-08 -5.6315745E-08 gauss-seidel spectral radius is 0.9903698 estimated iterations to convergence 83 setup time was (sec) 0.3600000 now iterating at: 14:16:13 rms-change max change #iterations 0.2477261 42.16383 at 10iterations 3.2849912E-02 4.504477 at 20iterations 4.4378238E-03 0.5709839 at 30iterations 5.8514439E-04 7.4205399E-02 at 40iterations 7.8691686E-05 9.6514225E-03 at 50iterations finished qdiffx linear iterations at : 14:16:16 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 7.8691686E-05 9.6514225E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 14:16:16 3.346u 0.159s 0:04.04 86.3% 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 Mon Oct 10 2011 at 14:16:16 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2160 !!! WARNING: SEP 119 has a net charge of -0.4750 !!! WARNING: GLM 120 has a net charge of -0.0940 !!! WARNING: HIT 142 has a net charge of 0.5140 !!! WARNING: MG3 318 has a net charge of 1.4000 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: 2.207478 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): 15.05800 54.48400 ymin,ymax (A): -7.529000 40.85200 zmin,zma (A): -5.098000 38.51800 x,y,z range (A): 39.42599 48.38100 43.61600 scale (grids/A): 2.207478 object centre (A): 34.77100 16.66150 16.71000 number of atom coordinates read : 2160 total number of charged atoms : 2022 net assigned charge : -3.154987 assigned positive charge : 325.9306 centred at (gu) : 87.39128 91.64906 87.34975 assigned negative charge : -329.0859 centred at (gu) : 87.43853 91.58939 87.34822 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 81843 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16721 grid for indexing accessible points = 1.400000 m= 34294 mr = 59178 m= 7920 mr = 26942 m= 917 mr = 5893 m= 31 mr = 582 m= 0 mr = 7 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 5249 time to turn everything in is 0.4100000 number of dielectric boundary points 32403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 47 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 16105 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) : 0.7358260 object centre at (A) : 34.77100 16.66150 16.71000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8351830E-02 5.2620945E-03 midg,1,midg; midg,igrid,midg 2.4714938E-04 -2.5233885E-02 1,midg,midg; igrid,midg,midg -1.1072394E-02 -2.6449999E-02 gauss-seidel spectral radius is 0.9989025 estimated iterations to convergence 239 setup time was (sec) 0.6300000 now iterating at: 14:16:17 rms-change max change #iterations 5.150853 199.9613 at 10iterations 2.603390 81.77552 at 20iterations 1.323121 43.37155 at 30iterations 0.6725434 18.45926 at 40iterations 0.3408195 9.490425 at 50iterations 0.1727678 5.425624 at 60iterations 8.7593079E-02 2.739251 at 70iterations 4.4496771E-02 1.219167 at 80iterations 2.2504894E-02 0.5986671 at 90iterations 1.1415968E-02 0.3234787 at 100iterations 5.7908003E-03 0.1657572 at 110iterations 2.9335145E-03 8.3410263E-02 at 120iterations finished qdiffx linear iterations at : 14:16:24 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 2.9335145E-03 8.3410263E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 14:16:25 7.846u 0.183s 0:08.42 95.2% 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 Mon Oct 10 2011 at 14:16:25 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2160 !!! WARNING: SEP 119 has a net charge of -0.4750 !!! WARNING: GLM 120 has a net charge of -0.0940 !!! WARNING: HIT 142 has a net charge of 0.5140 !!! WARNING: MG3 318 has a net charge of 1.4000 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: 3.311217 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): 15.05800 54.48400 ymin,ymax (A): -7.529000 40.85200 zmin,zma (A): -5.098000 38.51800 x,y,z range (A): 39.42599 48.38100 43.61600 scale (grids/A): 3.311217 object centre (A): 34.77100 16.66150 16.71000 number of atom coordinates read : 2160 total number of charged atoms : 2022 net assigned charge : -3.154987 assigned positive charge : 325.9306 centred at (gu) : 86.08688 92.47366 86.02463 assigned negative charge : -329.0859 centred at (gu) : 86.15773 92.38416 86.02226 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 188597 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16721 grid for indexing accessible points = 1.400000 m= 103976 mr = 141813 m= 46926 mr = 88270 m= 15759 mr = 39958 m= 3739 mr = 13079 m= 530 mr = 2996 m= 22 mr = 401 m= 0 mr = 3 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 18140 time to turn everything in is 1.270000 number of dielectric boundary points 73029 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 16176 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) : 2.207478 object centre at (A) : 34.77100 16.66150 16.71000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2672716 0.2089802 midg,1,midg; midg,igrid,midg -0.1640548 -0.3251844 1,midg,midg; igrid,midg,midg -1.0513507E-02 -0.2737652 gauss-seidel spectral radius is 0.9993048 estimated iterations to convergence 299 setup time was (sec) 1.500000 now iterating at: 14:16:27 rms-change max change #iterations 11.09384 259.1208 at 10iterations 6.530064 114.1958 at 20iterations 3.830265 76.37785 at 30iterations 2.249635 38.82069 at 40iterations 1.320118 22.97608 at 50iterations 0.7737832 12.41854 at 60iterations 0.4525286 7.446306 at 70iterations 0.2650037 4.113077 at 80iterations 0.1550847 2.554918 at 90iterations 9.0607606E-02 1.445389 at 100iterations 5.3237859E-02 0.8919199 at 110iterations 3.1098401E-02 0.5565052 at 120iterations 1.8223118E-02 0.3241806 at 130iterations 1.0660902E-02 0.1657715 at 140iterations 6.2596099E-03 0.1015129 at 150iterations 3.6789321E-03 5.9820175E-02 at 160iterations 2.1770585E-03 3.5837173E-02 at 170iterations 1.2904915E-03 2.0380616E-02 at 180iterations finished qdiffx linear iterations at : 14:16:38 total time elapsed so far: 12.86000 # loops : 180 mean,max change (kT/e) : 1.2904915E-03 2.0380616E-02 energy calculations done at 12.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.99000 DelPhi exited at 14:16:39 12.994u 0.203s 0:13.74 95.9% 0+0k 0+0io 0pf+0w