Mon Oct 10 17:05:12 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 17:05:12 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3667 !!! WARNING: HIT 104 has a net charge of 0.5140 !!! WARNING: HIR 145 has a net charge of 0.5140 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: 0.5206581 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): -17.41100 50.96400 ymin,ymax (A): -27.45600 29.10000 zmin,zma (A): -22.60400 38.13100 x,y,z range (A): 68.37500 56.55600 60.73500 scale (grids/A): 0.5206581 object centre (A): 16.77650 0.8220005 7.763498 number of atom coordinates read : 3667 total number of charged atoms : 3520 net assigned charge : 2.8038204E-02 assigned positive charge : 564.6057 centred at (gu) : 90.03046 88.12865 88.61194 assigned negative charge : -564.5797 centred at (gu) : 89.99936 87.97488 88.62905 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6468 nv = 96 ne = 84 npr = 69808 no. pairs analyzed = 69808 no. exposed pairs = 5103 no. arc points = 37305 no. surface atoms = 1707 nbur = 1960 mkacc time = 0.1900000 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= 239 mr = 2958 m= 0 mr = 3 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3746 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3693 ## 580 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8637 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1238198E-11 -2.9961082E-11 midg,1,midg; midg,igrid,midg -7.8454415E-10 2.9385358E-10 1,midg,midg; igrid,midg,midg -8.6031599E-11 1.0714465E-10 gauss-seidel spectral radius is 0.9810684 estimated iterations to convergence 60 setup time was (sec) 0.6900000 now iterating at: 17:05:13 rms-change max change #iterations 6.4388022E-02 13.69549 at 10iterations 3.7009995E-03 0.7891541 at 20iterations 2.2201457E-04 4.4914246E-02 at 30iterations 1.3655240E-05 2.8991699E-03 at 40iterations 9.6094686E-07 1.7929077E-04 at 50iterations finished qdiffx linear iterations at : 17:05:17 total time elapsed so far: 4.490000 # loops : 50 mean,max change (kT/e) : 9.6094686E-07 1.7929077E-04 energy calculations done at 4.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.650000 DelPhi exited at 17:05:18 4.653u 0.381s 0:05.52 91.1% 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 Mon Oct 10 2011 at 17:05:18 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3667 !!! WARNING: HIT 104 has a net charge of 0.5140 !!! WARNING: HIR 145 has a net charge of 0.5140 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: 1.561974 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): -17.41100 50.96400 ymin,ymax (A): -27.45600 29.10000 zmin,zma (A): -22.60400 38.13100 x,y,z range (A): 68.37500 56.55600 60.73500 scale (grids/A): 1.561974 object centre (A): 16.77650 0.8220005 7.763498 number of atom coordinates read : 3667 total number of charged atoms : 3520 net assigned charge : 2.8038204E-02 assigned positive charge : 564.6057 centred at (gu) : 90.09018 84.38464 85.83469 assigned negative charge : -564.5797 centred at (gu) : 89.99765 83.92455 85.88670 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 71970 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37305 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 19074 mr = 45421 m= 1466 mr = 11715 m= 25 mr = 494 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1365 time to turn everything in is 0.5800000 number of dielectric boundary points 34905 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 519 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 26542 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) : 0.5206581 object centre at (A) : 16.77650 0.8220005 7.763498 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5792537E-02 3.3313804E-03 midg,1,midg; midg,igrid,midg -6.8228389E-03 4.0810239E-03 1,midg,midg; igrid,midg,midg -2.5904404E-02 -1.3049175E-02 gauss-seidel spectral radius is 0.9980965 estimated iterations to convergence 182 setup time was (sec) 0.9400000 now iterating at: 17:05:19 rms-change max change #iterations 3.446016 163.8546 at 10iterations 1.399029 53.84102 at 20iterations 0.5686920 24.10035 at 30iterations 0.2310869 9.136831 at 40iterations 9.3996048E-02 3.358125 at 50iterations 3.8404319E-02 1.511164 at 60iterations 1.5667537E-02 0.6173449 at 70iterations 6.4041517E-03 0.2204585 at 80iterations 2.6032503E-03 9.4633102E-02 at 90iterations 1.0623914E-03 3.5366058E-02 at 100iterations 4.3359835E-04 1.5925407E-02 at 110iterations 1.7615336E-04 6.2046051E-03 at 120iterations finished qdiffx linear iterations at : 17:05:29 total time elapsed so far: 10.38000 # loops : 120 mean,max change (kT/e) : 1.7615336E-04 6.2046051E-03 energy calculations done at 10.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.54000 DelPhi exited at 17:05:29 10.547u 0.443s 0:11.65 94.2% 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 17:05:29 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3667 !!! WARNING: HIT 104 has a net charge of 0.5140 !!! WARNING: HIR 145 has a net charge of 0.5140 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: 2.342962 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): -17.41100 50.96400 ymin,ymax (A): -27.45600 29.10000 zmin,zma (A): -22.60400 38.13100 x,y,z range (A): 68.37500 56.55600 60.73500 scale (grids/A): 2.342962 object centre (A): 16.77650 0.8220005 7.763498 number of atom coordinates read : 3667 total number of charged atoms : 3520 net assigned charge : 2.8038204E-02 assigned positive charge : 564.6057 centred at (gu) : 90.13494 81.57669 83.75195 assigned negative charge : -564.5797 centred at (gu) : 89.99633 80.88669 83.82992 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 167614 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37305 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 68348 mr = 112583 m= 16193 mr = 50785 m= 1825 mr = 10923 m= 79 mr = 949 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 4170 time to turn everything in is 1.420000 number of dielectric boundary points 78801 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 28098 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) : 1.561974 object centre at (A) : 16.77650 0.8220005 7.763498 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2756489 5.4929428E-02 midg,1,midg; midg,igrid,midg -6.1145380E-02 3.1385757E-02 1,midg,midg; igrid,midg,midg -0.6219038 -0.5046594 gauss-seidel spectral radius is 0.9991350 estimated iterations to convergence 269 setup time was (sec) 1.810000 now iterating at: 17:05:32 rms-change max change #iterations 9.298582 311.5843 at 10iterations 5.262940 181.0910 at 20iterations 2.944245 79.36328 at 30iterations 1.636289 37.15820 at 40iterations 0.9082219 20.99506 at 50iterations 0.5031641 10.75683 at 60iterations 0.2775126 5.795198 at 70iterations 0.1529389 3.106987 at 80iterations 8.4104121E-02 2.033669 at 90iterations 4.6245538E-02 1.070903 at 100iterations 2.5404699E-02 0.5083981 at 110iterations 1.3948450E-02 0.3041379 at 120iterations 7.6616635E-03 0.1519985 at 130iterations 4.1929446E-03 8.8396072E-02 at 140iterations 2.3047987E-03 4.9699783E-02 at 150iterations 1.2667327E-03 2.4918079E-02 at 160iterations 6.9419603E-04 1.4165640E-02 at 170iterations 3.8081562E-04 8.4333420E-03 at 180iterations finished qdiffx linear iterations at : 17:05:48 total time elapsed so far: 18.04000 # loops : 180 mean,max change (kT/e) : 3.8081562E-04 8.4333420E-03 energy calculations done at 18.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.21000 DelPhi exited at 17:05:49 18.212u 0.464s 0:19.38 96.3% 0+0k 0+0io 0pf+0w