Sun Oct 9 15:41:53 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 15:41:54 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5310 !!! WARNING: HIZ 669 has a net charge of 0.2000 !!! WARNING: ZN7 731 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5201637 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): 67.07600 134.2270 ymin,ymax (A): -11.60700 56.83300 zmin,zma (A): -3.208000 63.63600 x,y,z range (A): 67.15099 68.44000 66.84399 scale (grids/A): 0.5201637 object centre (A): 100.6515 22.61300 30.21400 number of atom coordinates read : 5310 total number of charged atoms : 5139 net assigned charge : -2.399955 assigned positive charge : 812.5035 centred at (gu) : 89.78533 90.84914 90.84877 assigned negative charge : -814.9105 centred at (gu) : 89.79596 90.78734 90.91929 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8858 nv = 96 ne = 84 npr = 109047 no. pairs analyzed = 109047 no. exposed pairs = 6015 no. arc points = 42243 no. surface atoms = 2033 nbur = 3277 mkacc time = 0.2700000 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 = 1.652000 m= 325 mr = 4889 m= 4 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.5300000 number of dielectric boundary points 4281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4152 ## 586 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 11978 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0556734E-10 -4.5728873E-10 midg,1,midg; midg,igrid,midg -2.6188932E-10 2.7523087E-10 1,midg,midg; igrid,midg,midg -4.6452946E-12 -9.3142320E-11 gauss-seidel spectral radius is 0.9811227 estimated iterations to convergence 60 setup time was (sec) 0.7700000 now iterating at: 15:41:54 rms-change max change #iterations 7.8378625E-02 11.09433 at 10iterations 7.3778508E-03 1.201614 at 20iterations 2.2719384E-03 0.3881836 at 30iterations 8.6193875E-04 0.1478233 at 40iterations 3.2988141E-04 5.6678772E-02 at 50iterations finished qdiffx linear iterations at : 15:41:57 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 3.2988141E-04 5.6678772E-02 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 15:41:58 3.641u 0.172s 0:04.09 93.1% 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 15:41:58 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 = 5310 !!! WARNING: HIZ 669 has a net charge of 0.2000 !!! WARNING: ZN7 731 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: 1.560491 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): 67.07600 134.2270 ymin,ymax (A): -11.60700 56.83300 zmin,zma (A): -3.208000 63.63600 x,y,z range (A): 67.15099 68.44000 66.84399 scale (grids/A): 1.560491 object centre (A): 100.6515 22.61300 30.21400 number of atom coordinates read : 5310 total number of charged atoms : 5139 net assigned charge : -2.399955 assigned positive charge : 812.5035 centred at (gu) : 89.35430 92.54600 92.54474 assigned negative charge : -814.9105 centred at (gu) : 89.38778 92.36215 92.75773 start vw surface at 0.2100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 100624 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42243 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 30520 mr = 71628 m= 2880 mr = 21299 m= 62 mr = 1353 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 3000 time to turn everything in is 0.7300000 number of dielectric boundary points 39800 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 530 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 38859 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) : 0.5201637 object centre at (A) : 100.6515 22.61300 30.21400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2644367E-03 -6.4870487E-03 midg,1,midg; midg,igrid,midg -1.0964549E-02 2.1498624E-02 1,midg,midg; igrid,midg,midg -3.4041028E-02 -1.3967053E-02 gauss-seidel spectral radius is 0.9982181 estimated iterations to convergence 188 setup time was (sec) 1.060000 now iterating at: 15:41:59 rms-change max change #iterations 4.271415 143.8293 at 10iterations 1.793284 53.54839 at 20iterations 0.7537798 21.57330 at 30iterations 0.3188315 9.707760 at 40iterations 0.1346633 4.296448 at 50iterations 5.7427775E-02 1.721605 at 60iterations 2.4792535E-02 0.7764168 at 70iterations 1.1204599E-02 0.4204178 at 80iterations 5.5302964E-03 0.2200546 at 90iterations 3.0979030E-03 0.1165085 at 100iterations 1.9533953E-03 7.2540283E-02 at 110iterations 1.3257626E-03 4.9880981E-02 at 120iterations finished qdiffx linear iterations at : 15:42:05 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 1.3257626E-03 4.9880981E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 15:42:06 7.912u 0.178s 0:08.38 96.4% 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 15:42:06 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 = 5310 !!! WARNING: HIZ 669 has a net charge of 0.2000 !!! WARNING: ZN7 731 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.340736 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): 67.07600 134.2270 ymin,ymax (A): -11.60700 56.83300 zmin,zma (A): -3.208000 63.63600 x,y,z range (A): 67.15099 68.44000 66.84399 scale (grids/A): 2.340736 object centre (A): 100.6515 22.61300 30.21400 number of atom coordinates read : 5310 total number of charged atoms : 5139 net assigned charge : -2.399955 assigned positive charge : 812.5035 centred at (gu) : 89.03101 93.81840 93.81670 assigned negative charge : -814.9105 centred at (gu) : 89.08163 93.54328 94.13647 start vw surface at 0.2200000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 234761 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42243 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 107905 mr = 174989 m= 29226 mr = 86691 m= 4425 mr = 22159 m= 243 mr = 2837 m= 2 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 9562 time to turn everything in is 1.830000 number of dielectric boundary points 89791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 51 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 41028 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) : 1.560491 object centre at (A) : 100.6515 22.61300 30.21400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1766970 -2.2896444E-02 midg,1,midg; midg,igrid,midg -0.1892824 0.6817343 1,midg,midg; igrid,midg,midg -0.6772668 -0.2567927 gauss-seidel spectral radius is 0.9991940 estimated iterations to convergence 278 setup time was (sec) 2.150000 now iterating at: 15:42:08 rms-change max change #iterations 11.27202 362.2637 at 10iterations 6.485502 167.2040 at 20iterations 3.706676 82.13821 at 30iterations 2.112964 54.77777 at 40iterations 1.198296 24.11004 at 50iterations 0.6792265 12.62979 at 60iterations 0.3842041 7.194004 at 70iterations 0.2169611 4.001175 at 80iterations 0.1220409 2.127638 at 90iterations 6.8902850E-02 1.253773 at 100iterations 3.8738202E-02 0.6859112 at 110iterations 2.1891298E-02 0.4059868 at 120iterations 1.2404895E-02 0.2158909 at 130iterations 7.0807687E-03 0.1243954 at 140iterations 4.0887957E-03 7.8735352E-02 at 150iterations 2.4233288E-03 4.7363281E-02 at 160iterations 1.4956541E-03 3.1692505E-02 at 170iterations 9.7824098E-04 2.0866394E-02 at 180iterations finished qdiffx linear iterations at : 15:42:19 total time elapsed so far: 13.05000 # loops : 180 mean,max change (kT/e) : 9.7824098E-04 2.0866394E-02 energy calculations done at 13.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.26000 DelPhi exited at 15:42:20 13.260u 0.204s 0:13.77 97.7% 0+0k 0+0io 0pf+0w