Sun Oct 9 15:42:23 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+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 Sun Oct 9 2011 at 15:42:23 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5138 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3961 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5331256 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): 8.352000 63.64900 ymin,ymax (A): 58.55900 124.8780 zmin,zma (A): 29.60900 96.38500 x,y,z range (A): 55.29700 66.31900 66.77600 scale (grids/A): 0.5331256 object centre (A): 36.00050 91.71850 62.99700 number of atom coordinates read : 5138 total number of charged atoms : 4974 net assigned charge : 6.100028 assigned positive charge : 798.4271 centred at (gu) : 89.16135 89.06202 90.63764 assigned negative charge : -792.3337 centred at (gu) : 89.19489 88.99215 90.51965 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 9118 nv = 96 ne = 84 npr = 103416 no. pairs analyzed = 103416 no. exposed pairs = 6184 no. arc points = 43282 no. surface atoms = 2086 nbur = 3052 mkacc time = 0.2200000 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= 357 mr = 4910 m= 0 mr = 12 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.4700000 number of dielectric boundary points 4553 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4307 ## 607 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 12256 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4351418E-10 1.2523701E-09 midg,1,midg; midg,igrid,midg -3.6726222E-10 5.7183447E-10 1,midg,midg; igrid,midg,midg 5.7530991E-10 -1.3876961E-11 gauss-seidel spectral radius is 0.9820206 estimated iterations to convergence 61 setup time was (sec) 0.6800000 now iterating at: 15:42:24 rms-change max change #iterations 8.8367790E-02 11.62326 at 10iterations 6.2924288E-03 0.8755684 at 20iterations 1.0384904E-03 0.1189733 at 30iterations 3.4636035E-04 4.8817635E-02 at 40iterations 1.2437892E-04 1.9531727E-02 at 50iterations finished qdiffx linear iterations at : 15:42:26 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 1.2437892E-04 1.9531727E-02 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 15:42:27 3.276u 0.148s 0:03.77 90.4% 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 Sun Oct 9 2011 at 15:42:27 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5138 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3961 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.599377 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): 8.352000 63.64900 ymin,ymax (A): 58.55900 124.8780 zmin,zma (A): 29.60900 96.38500 x,y,z range (A): 55.29700 66.31900 66.77600 scale (grids/A): 1.599377 object centre (A): 36.00050 91.71850 62.99700 number of atom coordinates read : 5138 total number of charged atoms : 4974 net assigned charge : 6.100028 assigned positive charge : 798.4271 centred at (gu) : 87.48231 87.18428 91.91093 assigned negative charge : -792.3337 centred at (gu) : 87.58421 86.97626 91.55885 start vw surface at 0.2200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 102588 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43282 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 31499 mr = 71643 m= 3025 mr = 21866 m= 72 mr = 1466 m= 0 mr = 11 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 2428 time to turn everything in is 0.6900000 number of dielectric boundary points 42198 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 568 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 37857 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) : 0.5331256 object centre at (A) : 36.00050 91.71850 62.99700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2721544E-03 2.1251276E-02 midg,1,midg; midg,igrid,midg -3.9455939E-02 1.9795790E-02 1,midg,midg; igrid,midg,midg 5.6136390E-03 2.8569656E-03 gauss-seidel spectral radius is 0.9983091 estimated iterations to convergence 193 setup time was (sec) 0.9600000 now iterating at: 15:42:28 rms-change max change #iterations 4.430241 172.2523 at 10iterations 1.900454 61.76716 at 20iterations 0.8156613 26.01257 at 30iterations 0.3519010 11.07798 at 40iterations 0.1513360 4.424793 at 50iterations 6.5457098E-02 1.911053 at 60iterations 2.8167281E-02 0.8306275 at 70iterations 1.2278672E-02 0.3299417 at 80iterations 5.3611691E-03 0.1564522 at 90iterations 2.4022621E-03 8.0581665E-02 at 100iterations 1.1243938E-03 3.5202920E-02 at 110iterations 5.6639808E-04 1.7378807E-02 at 120iterations finished qdiffx linear iterations at : 15:42:34 total time elapsed so far: 6.990000 # loops : 120 mean,max change (kT/e) : 5.6639808E-04 1.7378807E-02 energy calculations done at 6.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.160000 DelPhi exited at 15:42:35 7.164u 0.161s 0:07.64 95.8% 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 Sun Oct 9 2011 at 15:42:35 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5138 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3961 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.399065 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): 8.352000 63.64900 ymin,ymax (A): 58.55900 124.8780 zmin,zma (A): 29.60900 96.38500 x,y,z range (A): 55.29700 66.31900 66.77600 scale (grids/A): 2.399065 object centre (A): 36.00050 91.71850 62.99700 number of atom coordinates read : 5138 total number of charged atoms : 4974 net assigned charge : 6.100028 assigned positive charge : 798.4271 centred at (gu) : 86.22315 85.77605 92.86563 assigned negative charge : -792.3337 centred at (gu) : 86.37634 85.46429 92.33820 start vw surface at 0.2100000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 239107 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43282 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 110090 mr = 175731 m= 30532 mr = 87688 m= 4623 mr = 22957 m= 291 mr = 2915 m= 3 mr = 142 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 7822 time to turn everything in is 1.650000 number of dielectric boundary points 95213 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 39728 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) : 1.599377 object centre at (A) : 36.00050 91.71850 62.99700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.5144859E-02 0.2914418 midg,1,midg; midg,igrid,midg -0.7811845 0.2094535 1,midg,midg; igrid,midg,midg 0.1138517 6.8093337E-02 gauss-seidel spectral radius is 0.9992254 estimated iterations to convergence 284 setup time was (sec) 1.940000 now iterating at: 15:42:37 rms-change max change #iterations 11.69013 340.0901 at 10iterations 6.843852 172.0886 at 20iterations 3.984703 93.74039 at 30iterations 2.303705 51.63448 at 40iterations 1.329818 26.48520 at 50iterations 0.7621468 14.25851 at 60iterations 0.4369287 8.175637 at 70iterations 0.2500371 4.582401 at 80iterations 0.1429075 2.596613 at 90iterations 8.1599638E-02 1.384371 at 100iterations 4.6640459E-02 0.8613358 at 110iterations 2.6511559E-02 0.4521103 at 120iterations 1.5091603E-02 0.2992191 at 130iterations 8.5979123E-03 0.1498756 at 140iterations 4.9041412E-03 8.5278511E-02 at 150iterations 2.7989454E-03 4.9179077E-02 at 160iterations 1.5996273E-03 2.6299387E-02 at 170iterations 9.1614266E-04 1.5552521E-02 at 180iterations finished qdiffx linear iterations at : 15:42:47 total time elapsed so far: 11.91000 # loops : 180 mean,max change (kT/e) : 9.1614266E-04 1.5552521E-02 energy calculations done at 11.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.08000 DelPhi exited at 15:42:47 12.079u 0.169s 0:12.51 97.7% 0+0k 0+0io 0pf+0w