Sat Oct 8 18:27:55 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 Sat Oct 8 2011 at 18:27:55 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN5 556 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6226062 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): -32.08400 17.44400 ymin,ymax (A): -23.46000 22.89300 zmin,zma (A): -12.55100 44.62800 x,y,z range (A): 49.52800 46.35300 57.17900 scale (grids/A): 0.6226062 object centre (A): -7.320000 -0.2834997 16.03850 number of atom coordinates read : 2586 total number of charged atoms : 2453 net assigned charge : 4.500009 assigned positive charge : 391.4040 centred at (gu) : 88.57241 89.18759 89.89468 assigned negative charge : -386.9045 centred at (gu) : 88.47588 89.25288 89.76382 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6513 nv = 96 ne = 84 npr = 54199 no. pairs analyzed = 54199 no. exposed pairs = 2921 no. arc points = 20824 no. surface atoms = 991 nbur = 1595 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 319 mr = 3706 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 95 time to turn everything in is 0.3100000 number of dielectric boundary points 3087 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2108 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8107 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5944462E-09 1.2888342E-08 midg,1,midg; midg,igrid,midg 1.0301817E-08 -5.3870208E-10 1,midg,midg; igrid,midg,midg -4.1664689E-09 7.9220026E-09 gauss-seidel spectral radius is 0.9866322 estimated iterations to convergence 71 setup time was (sec) 0.5300000 now iterating at: 18:27:56 rms-change max change #iterations 0.1294075 19.80103 at 10iterations 1.2144017E-02 1.905107 at 20iterations 1.1294197E-03 0.1590233 at 30iterations 1.0466545E-04 1.4560699E-02 at 40iterations 9.6649983E-06 1.2736320E-03 at 50iterations finished qdiffx linear iterations at : 18:27:59 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 9.6649983E-06 1.2736320E-03 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.150000 DelPhi exited at 18:27:59 3.152u 0.133s 0:03.58 91.6% 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 Sat Oct 8 2011 at 18:27:59 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN5 556 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.867819 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): -32.08400 17.44400 ymin,ymax (A): -23.46000 22.89300 zmin,zma (A): -12.55100 44.62800 x,y,z range (A): 49.52800 46.35300 57.17900 scale (grids/A): 1.867819 object centre (A): -7.320000 -0.2834997 16.03850 number of atom coordinates read : 2586 total number of charged atoms : 2453 net assigned charge : 4.500009 assigned positive charge : 391.4040 centred at (gu) : 85.71693 87.56230 89.68340 assigned negative charge : -386.9045 centred at (gu) : 85.42734 87.75840 89.29125 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 70844 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20824 grid for indexing accessible points = 1.400000 m= 25007 mr = 50002 m= 3621 mr = 18647 m= 183 mr = 2319 m= 3 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 5161 time to turn everything in is 0.5100000 number of dielectric boundary points 28617 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 19216 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) : 0.6226062 object centre at (A) : -7.320000 -0.2834997 16.03850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5082981E-02 2.4825918E-02 midg,1,midg; midg,igrid,midg 1.4804048E-02 -1.0492057E-03 1,midg,midg; igrid,midg,midg -2.6780481E-03 3.2474078E-02 gauss-seidel spectral radius is 0.9985741 estimated iterations to convergence 210 setup time was (sec) 0.7800000 now iterating at: 18:28:00 rms-change max change #iterations 4.047493 192.4531 at 10iterations 1.860526 65.86181 at 20iterations 0.8561560 31.68378 at 30iterations 0.3946973 12.56736 at 40iterations 0.1818897 6.260489 at 50iterations 8.4006041E-02 2.701576 at 60iterations 3.8757510E-02 1.238558 at 70iterations 1.7903741E-02 0.5725784 at 80iterations 8.2220435E-03 0.2904682 at 90iterations 3.7906070E-03 0.1255131 at 100iterations 1.7457107E-03 6.2227249E-02 at 110iterations 8.0372259E-04 2.5733948E-02 at 120iterations finished qdiffx linear iterations at : 18:28:06 total time elapsed so far: 6.720000 # loops : 120 mean,max change (kT/e) : 8.0372259E-04 2.5733948E-02 energy calculations done at 6.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.900000 DelPhi exited at 18:28:06 6.899u 0.167s 0:07.35 95.9% 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 Sat Oct 8 2011 at 18:28:07 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN5 556 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.801728 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): -32.08400 17.44400 ymin,ymax (A): -23.46000 22.89300 zmin,zma (A): -12.55100 44.62800 x,y,z range (A): 49.52800 46.35300 57.17900 scale (grids/A): 2.801728 object centre (A): -7.320000 -0.2834997 16.03850 number of atom coordinates read : 2586 total number of charged atoms : 2453 net assigned charge : 4.500009 assigned positive charge : 391.4040 centred at (gu) : 83.57533 86.34344 89.52529 assigned negative charge : -386.9045 centred at (gu) : 83.14098 86.63759 88.93684 start vw surface at 0.1400000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 163860 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20824 grid for indexing accessible points = 1.400000 m= 82598 mr = 120678 m= 28077 mr = 68422 m= 6530 mr = 22743 m= 821 mr = 5041 m= 54 mr = 559 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 16496 time to turn everything in is 1.190000 number of dielectric boundary points 64473 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 19622 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) : 1.867819 object centre at (A) : -7.320000 -0.2834997 16.03850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.8157382E-02 0.2979992 midg,1,midg; midg,igrid,midg 0.1630567 -2.6566068E-02 1,midg,midg; igrid,midg,midg 1.4553138E-02 0.4267416 gauss-seidel spectral radius is 0.9992348 estimated iterations to convergence 285 setup time was (sec) 1.470000 now iterating at: 18:28:08 rms-change max change #iterations 9.453699 374.8142 at 10iterations 5.384635 103.4891 at 20iterations 3.062583 66.06660 at 30iterations 1.740553 35.51823 at 40iterations 0.9888402 17.33735 at 50iterations 0.5597705 10.71433 at 60iterations 0.3191014 5.996412 at 70iterations 0.1808213 3.357861 at 80iterations 0.1028377 1.964038 at 90iterations 5.8347207E-02 1.054747 at 100iterations 3.3172574E-02 0.6326070 at 110iterations 1.8859366E-02 0.3606758 at 120iterations 1.0695299E-02 0.2144089 at 130iterations 6.0860594E-03 0.1128254 at 140iterations 3.4544345E-03 6.2770844E-02 at 150iterations 1.9618303E-03 4.1152954E-02 at 160iterations 1.1195117E-03 2.0584106E-02 at 170iterations 6.3506502E-04 1.2767792E-02 at 180iterations finished qdiffx linear iterations at : 18:28:17 total time elapsed so far: 10.82000 # loops : 180 mean,max change (kT/e) : 6.3506502E-04 1.2767792E-02 energy calculations done at 10.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.00000 DelPhi exited at 18:28:18 10.998u 0.164s 0:11.43 97.5% 0+0k 0+0io 0pf+0w