Sun Oct 9 13:30:25 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 Sun Oct 9 2011 at 13:30:25 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2375 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: 0.6755987 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): -6.819000 44.60800 ymin,ymax (A): -14.19500 38.49900 zmin,zma (A): 1.418000 44.54900 x,y,z range (A): 51.42700 52.69400 43.13100 scale (grids/A): 0.6755987 object centre (A): 18.89450 12.15200 22.98350 number of atom coordinates read : 2375 total number of charged atoms : 2234 net assigned charge : 3.500019 assigned positive charge : 364.6372 centred at (gu) : 89.55578 90.74202 90.99739 assigned negative charge : -361.1376 centred at (gu) : 89.54421 90.90115 91.04968 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7340 nv = 96 ne = 84 npr = 47503 no. pairs analyzed = 47503 no. exposed pairs = 3034 no. arc points = 21315 no. surface atoms = 1014 nbur = 1361 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 394 mr = 3983 m= 3 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3704 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2066 ## 194 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8470 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3009564E-08 -5.4441529E-10 midg,1,midg; midg,igrid,midg 4.8560437E-08 -3.5108989E-08 1,midg,midg; igrid,midg,midg 1.1828818E-08 1.5690206E-08 gauss-seidel spectral radius is 0.9886216 estimated iterations to convergence 76 setup time was (sec) 0.5100000 now iterating at: 13:30:25 rms-change max change #iterations 0.1766932 25.45353 at 10iterations 2.0092094E-02 3.257466 at 20iterations 2.8995182E-03 0.4561234 at 30iterations 7.0167327E-04 0.1164169 at 40iterations 2.3232779E-04 3.8677216E-02 at 50iterations finished qdiffx linear iterations at : 13:30:28 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 2.3232779E-04 3.8677216E-02 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 13:30:28 3.125u 0.121s 0:03.51 92.3% 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 Sun Oct 9 2011 at 13:30:28 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2375 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: 2.026796 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): -6.819000 44.60800 ymin,ymax (A): -14.19500 38.49900 zmin,zma (A): 1.418000 44.54900 x,y,z range (A): 51.42700 52.69400 43.13100 scale (grids/A): 2.026796 object centre (A): 18.89450 12.15200 22.98350 number of atom coordinates read : 2375 total number of charged atoms : 2234 net assigned charge : 3.500019 assigned positive charge : 364.6372 centred at (gu) : 88.66687 92.22552 92.99176 assigned negative charge : -361.1376 centred at (gu) : 88.63229 92.70325 93.14895 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 78505 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21315 grid for indexing accessible points = 1.400000 m= 29219 mr = 54321 m= 4805 mr = 21378 m= 367 mr = 2925 m= 6 mr = 167 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 34111 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 123 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 17671 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) : 0.6755987 object centre at (A) : 18.89450 12.15200 22.98350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8409576E-02 1.0427078E-02 midg,1,midg; midg,igrid,midg 1.3933286E-02 -4.7594931E-02 1,midg,midg; igrid,midg,midg 3.9340775E-02 -8.1908330E-03 gauss-seidel spectral radius is 0.9987707 estimated iterations to convergence 226 setup time was (sec) 0.8300000 now iterating at: 13:30:29 rms-change max change #iterations 4.666294 200.7603 at 10iterations 2.259734 82.18214 at 20iterations 1.098680 33.04196 at 30iterations 0.5350370 17.27338 at 40iterations 0.2605384 7.610920 at 50iterations 0.1271271 4.169168 at 60iterations 6.2293444E-02 2.009717 at 70iterations 3.0347558E-02 0.9074707 at 80iterations 1.4971052E-02 0.4582748 at 90iterations 7.5007090E-03 0.2296524 at 100iterations 3.8372779E-03 0.1188889 at 110iterations 2.0468906E-03 6.6997170E-02 at 120iterations finished qdiffx linear iterations at : 13:30:35 total time elapsed so far: 6.790000 # loops : 120 mean,max change (kT/e) : 2.0468906E-03 6.6997170E-02 energy calculations done at 6.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.960000 DelPhi exited at 13:30:36 6.964u 0.149s 0:07.43 95.5% 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 13:30:36 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2375 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: 3.040194 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): -6.819000 44.60800 ymin,ymax (A): -14.19500 38.49900 zmin,zma (A): 1.418000 44.54900 x,y,z range (A): 51.42700 52.69400 43.13100 scale (grids/A): 3.040194 object centre (A): 18.89450 12.15200 22.98350 number of atom coordinates read : 2375 total number of charged atoms : 2234 net assigned charge : 3.500019 assigned positive charge : 364.6372 centred at (gu) : 88.00023 93.33823 94.48761 assigned negative charge : -361.1376 centred at (gu) : 87.94849 94.05490 94.72338 start vw surface at 0.1600000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 181389 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21315 grid for indexing accessible points = 1.400000 m= 93738 mr = 131646 m= 34479 mr = 76450 m= 8529 mr = 27405 m= 1472 mr = 6289 m= 162 mr = 999 m= 5 mr = 97 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.440000 number of dielectric boundary points 76888 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 17871 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) : 2.026796 object centre at (A) : 18.89450 12.15200 22.98350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4053995 -1.5307593E-02 midg,1,midg; midg,igrid,midg 0.2784333 -0.6365350 1,midg,midg; igrid,midg,midg 0.5011571 -0.3165275 gauss-seidel spectral radius is 0.9992853 estimated iterations to convergence 295 setup time was (sec) 1.720000 now iterating at: 13:30:38 rms-change max change #iterations 10.63523 426.4700 at 10iterations 6.282200 119.4200 at 20iterations 3.718630 80.28804 at 30iterations 2.188525 44.23592 at 40iterations 1.285004 22.33208 at 50iterations 0.7524432 14.09193 at 60iterations 0.4405422 7.850908 at 70iterations 0.2571952 4.566786 at 80iterations 0.1505789 2.950183 at 90iterations 8.7957636E-02 1.539968 at 100iterations 5.1565740E-02 0.9835472 at 110iterations 3.0250791E-02 0.5544567 at 120iterations 1.7935663E-02 0.3514099 at 130iterations 1.0837873E-02 0.2095623 at 140iterations 6.7346222E-03 0.1301184 at 150iterations 4.3890034E-03 9.0999603E-02 at 160iterations 3.0397263E-03 7.0037842E-02 at 170iterations 2.2417263E-03 5.8029175E-02 at 180iterations finished qdiffx linear iterations at : 13:30:47 total time elapsed so far: 11.29000 # loops : 180 mean,max change (kT/e) : 2.2417263E-03 5.8029175E-02 energy calculations done at 11.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.50000 DelPhi exited at 13:30:48 11.500u 0.167s 0:11.93 97.7% 0+0k 0+0io 0pf+0w