Sat Oct 8 21:54:39 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 21:54:39 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6321135 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): -8.729000 43.87300 ymin,ymax (A): -21.39500 34.92400 zmin,zma (A): 2.973000 54.90400 x,y,z range (A): 52.60200 56.31900 51.93100 scale (grids/A): 0.6321135 object centre (A): 17.57200 6.764500 28.93850 number of atom coordinates read : 2593 total number of charged atoms : 2453 net assigned charge : 4.500002 assigned positive charge : 388.9100 centred at (gu) : 88.72540 89.33292 91.78889 assigned negative charge : -384.4105 centred at (gu) : 88.77531 89.27110 91.68869 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7028 nv = 96 ne = 84 npr = 51977 no. pairs analyzed = 51977 no. exposed pairs = 3340 no. arc points = 23621 no. surface atoms = 1116 nbur = 1477 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 377 mr = 3731 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3629 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2387 ## 248 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8479 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8955061E-09 2.0912605E-08 midg,1,midg; midg,igrid,midg -9.4905994E-10 9.2378247E-09 1,midg,midg; igrid,midg,midg 1.2600024E-08 3.1444525E-10 gauss-seidel spectral radius is 0.9870386 estimated iterations to convergence 72 setup time was (sec) 0.4000000 now iterating at: 21:54:39 rms-change max change #iterations 0.1382079 22.67196 at 10iterations 1.3134281E-02 2.038392 at 20iterations 1.2689243E-03 0.1774197 at 30iterations 1.2341341E-04 2.3301125E-02 at 40iterations 1.5087176E-05 2.0065308E-03 at 50iterations finished qdiffx linear iterations at : 21:54:42 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 1.5087176E-05 2.0065308E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 21:54:43 3.526u 0.186s 0:04.01 92.2% 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 Sat Oct 8 2011 at 21:54:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.896340 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): -8.729000 43.87300 ymin,ymax (A): -21.39500 34.92400 zmin,zma (A): 2.973000 54.90400 x,y,z range (A): 52.60200 56.31900 51.93100 scale (grids/A): 1.896340 object centre (A): 17.57200 6.764500 28.93850 number of atom coordinates read : 2593 total number of charged atoms : 2453 net assigned charge : 4.500002 assigned positive charge : 388.9100 centred at (gu) : 86.17575 87.99818 95.36649 assigned negative charge : -384.4105 centred at (gu) : 86.32575 87.81309 95.06573 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 75293 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23621 grid for indexing accessible points = 1.400000 m= 26674 mr = 51470 m= 4175 mr = 19018 m= 254 mr = 2517 m= 3 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 33297 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 174 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 19315 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) : 0.6321135 object centre at (A) : 17.57200 6.764500 28.93850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9446706E-02 2.4942044E-02 midg,1,midg; midg,igrid,midg -3.1822309E-02 1.3044541E-02 1,midg,midg; igrid,midg,midg 2.2353737E-02 1.7307449E-02 gauss-seidel spectral radius is 0.9986294 estimated iterations to convergence 214 setup time was (sec) 0.6200000 now iterating at: 21:54:44 rms-change max change #iterations 4.213426 174.6773 at 10iterations 1.974113 66.05100 at 20iterations 0.9273118 27.27179 at 30iterations 0.4345934 14.80824 at 40iterations 0.2029823 6.116274 at 50iterations 9.5292702E-02 3.261572 at 60iterations 4.4409540E-02 1.342745 at 70iterations 2.0824216E-02 0.6932373 at 80iterations 9.7220931E-03 0.3264694 at 90iterations 4.5727608E-03 0.1486950 at 100iterations 2.1400005E-03 6.8490982E-02 at 110iterations 1.0002721E-03 3.2901764E-02 at 120iterations finished qdiffx linear iterations at : 21:54:51 total time elapsed so far: 8.050000 # loops : 120 mean,max change (kT/e) : 1.0002721E-03 3.2901764E-02 energy calculations done at 8.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.180000 DelPhi exited at 21:54:51 8.179u 0.219s 0:08.67 96.6% 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 21:54:51 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.844511 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): -8.729000 43.87300 ymin,ymax (A): -21.39500 34.92400 zmin,zma (A): 2.973000 54.90400 x,y,z range (A): 52.60200 56.31900 51.93100 scale (grids/A): 2.844511 object centre (A): 17.57200 6.764500 28.93850 number of atom coordinates read : 2593 total number of charged atoms : 2453 net assigned charge : 4.500002 assigned positive charge : 388.9100 centred at (gu) : 84.26359 86.99717 98.04948 assigned negative charge : -384.4105 centred at (gu) : 84.48852 86.71953 97.59855 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 174601 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23621 grid for indexing accessible points = 1.400000 m= 86849 mr = 125567 m= 30568 mr = 69987 m= 7449 mr = 23760 m= 1160 mr = 5416 m= 73 mr = 783 m= 1 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9700000 number of dielectric boundary points 75150 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.080000 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) : 1.896340 object centre at (A) : 17.57200 6.764500 28.93850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3016052 0.2694391 midg,1,midg; midg,igrid,midg -0.7720753 0.1251724 1,midg,midg; igrid,midg,midg 0.3605534 9.6300520E-02 gauss-seidel spectral radius is 0.9992685 estimated iterations to convergence 292 setup time was (sec) 1.240000 now iterating at: 21:54:53 rms-change max change #iterations 10.06976 381.4215 at 10iterations 5.998823 142.8145 at 20iterations 3.546232 79.63146 at 30iterations 2.088879 46.40200 at 40iterations 1.220116 23.10812 at 50iterations 0.7147524 14.95920 at 60iterations 0.4162442 7.738914 at 70iterations 0.2418397 4.489754 at 80iterations 0.1401037 2.480397 at 90iterations 8.1274554E-02 1.526516 at 100iterations 4.7002077E-02 0.8249474 at 110iterations 2.7218919E-02 0.4889412 at 120iterations 1.5729325E-02 0.2797966 at 130iterations 9.0792421E-03 0.1624017 at 140iterations 5.2444516E-03 0.1139278 at 150iterations 3.0292226E-03 5.9668541E-02 at 160iterations 1.7446949E-03 3.2750607E-02 at 170iterations 1.0097821E-03 1.9318104E-02 at 180iterations finished qdiffx linear iterations at : 21:55:05 total time elapsed so far: 13.21000 # loops : 180 mean,max change (kT/e) : 1.0097821E-03 1.9318104E-02 energy calculations done at 13.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.34000 DelPhi exited at 21:55:05 13.340u 0.223s 0:13.84 97.9% 0+0k 0+0io 0pf+0w