Tue Oct 11 07:54:26 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 Tue Oct 11 2011 at 07:54:26 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 = 2380 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: 0.6379928 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): -1.888000 53.91200 ymin,ymax (A): -22.58300 22.78900 zmin,zma (A): 9.047999 54.72300 x,y,z range (A): 55.80000 45.37200 45.67500 scale (grids/A): 0.6379928 object centre (A): 26.01200 0.1029997 31.88550 number of atom coordinates read : 2380 total number of charged atoms : 2244 net assigned charge : 5.500007 assigned positive charge : 357.6723 centred at (gu) : 88.73310 90.34606 89.84753 assigned negative charge : -352.1728 centred at (gu) : 88.74407 90.29028 89.67072 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6513 nv = 96 ne = 84 npr = 48310 no. pairs analyzed = 48310 no. exposed pairs = 2865 no. arc points = 20169 no. surface atoms = 976 nbur = 1404 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 325 mr = 3610 m= 2 mr = 37 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 3193 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2024 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7749 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0852921E-08 2.4108671E-08 midg,1,midg; midg,igrid,midg 1.8288129E-09 1.4105450E-08 1,midg,midg; igrid,midg,midg 1.1294492E-08 4.9899547E-09 gauss-seidel spectral radius is 0.9872501 estimated iterations to convergence 72 setup time was (sec) 0.5100000 now iterating at: 07:54:27 rms-change max change #iterations 0.1401652 18.94432 at 10iterations 1.3618052E-02 1.891197 at 20iterations 1.4485883E-03 0.1986237 at 30iterations 1.6839169E-04 2.7423859E-02 at 40iterations 2.4171097E-05 4.0092468E-03 at 50iterations finished qdiffx linear iterations at : 07:54:29 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 2.4171097E-05 4.0092468E-03 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 07:54:30 3.073u 0.137s 0:03.86 82.9% 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 Tue Oct 11 2011 at 07:54:30 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 = 2380 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: 1.913978 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): -1.888000 53.91200 ymin,ymax (A): -22.58300 22.78900 zmin,zma (A): 9.047999 54.72300 x,y,z range (A): 55.80000 45.37200 45.67500 scale (grids/A): 1.913978 object centre (A): 26.01200 0.1029997 31.88550 number of atom coordinates read : 2380 total number of charged atoms : 2244 net assigned charge : 5.500007 assigned positive charge : 357.6723 centred at (gu) : 86.19879 91.03765 89.54232 assigned negative charge : -352.1728 centred at (gu) : 86.23215 90.87093 89.01180 start vw surface at 0.2100000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 69634 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20169 grid for indexing accessible points = 1.400000 m= 25457 mr = 48470 m= 3686 mr = 18848 m= 214 mr = 2130 m= 2 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 29472 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 17640 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) : 0.6379928 object centre at (A) : 26.01200 0.1029997 31.88550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6230745E-02 3.8893595E-02 midg,1,midg; midg,igrid,midg -1.8689159E-03 4.8917821E-03 1,midg,midg; igrid,midg,midg 2.1480141E-02 2.4993431E-02 gauss-seidel spectral radius is 0.9986243 estimated iterations to convergence 214 setup time was (sec) 0.8400000 now iterating at: 07:54:31 rms-change max change #iterations 4.065499 191.8634 at 10iterations 1.897074 67.16087 at 20iterations 0.8925806 35.57697 at 30iterations 0.4167241 13.70372 at 40iterations 0.1954922 6.726929 at 50iterations 9.1515042E-02 2.976871 at 60iterations 4.2815417E-02 1.487576 at 70iterations 1.9967142E-02 0.6299591 at 80iterations 9.4191711E-03 0.3456173 at 90iterations 4.4054249E-03 0.1506424 at 100iterations 2.0784116E-03 7.7880859E-02 at 110iterations 9.7990537E-04 3.3825874E-02 at 120iterations finished qdiffx linear iterations at : 07:54:37 total time elapsed so far: 7.310000 # loops : 120 mean,max change (kT/e) : 9.7990537E-04 3.3825874E-02 energy calculations done at 7.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.490000 DelPhi exited at 07:54:38 7.491u 0.206s 0:08.26 93.0% 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 Tue Oct 11 2011 at 07:54:38 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 = 2380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.870968 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): -1.888000 53.91200 ymin,ymax (A): -22.58300 22.78900 zmin,zma (A): 9.047999 54.72300 x,y,z range (A): 55.80000 45.37200 45.67500 scale (grids/A): 2.870968 object centre (A): 26.01200 0.1029997 31.88550 number of atom coordinates read : 2380 total number of charged atoms : 2244 net assigned charge : 5.500007 assigned positive charge : 357.6723 centred at (gu) : 84.29808 91.55646 89.31353 assigned negative charge : -352.1728 centred at (gu) : 84.34840 91.30640 88.51774 start vw surface at 0.2200000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 160823 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20169 grid for indexing accessible points = 1.400000 m= 82929 mr = 117135 m= 29676 mr = 68249 m= 6415 mr = 23633 m= 801 mr = 4598 m= 48 mr = 520 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.290000 number of dielectric boundary points 66533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 17944 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) : 1.913978 object centre at (A) : 26.01200 0.1029997 31.88550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2417828 0.3992289 midg,1,midg; midg,igrid,midg -2.6394175E-02 -2.6710229E-02 1,midg,midg; igrid,midg,midg 9.6967079E-02 0.1884959 gauss-seidel spectral radius is 0.9992481 estimated iterations to convergence 288 setup time was (sec) 1.560000 now iterating at: 07:54:40 rms-change max change #iterations 9.455515 371.2329 at 10iterations 5.491518 124.7094 at 20iterations 3.174696 73.89305 at 30iterations 1.829994 37.47324 at 40iterations 1.052111 22.63977 at 50iterations 0.6048067 12.01045 at 60iterations 0.3471243 6.382385 at 70iterations 0.1987849 3.666925 at 80iterations 0.1138214 2.302688 at 90iterations 6.5254383E-02 1.295378 at 100iterations 3.7439007E-02 0.7824337 at 110iterations 2.1374708E-02 0.4177818 at 120iterations 1.2265610E-02 0.2248144 at 130iterations 7.0286170E-03 0.1269760 at 140iterations 4.0212134E-03 7.3848724E-02 at 150iterations 2.3097887E-03 4.3981552E-02 at 160iterations 1.3239685E-03 2.6935577E-02 at 170iterations 7.6792995E-04 1.4671326E-02 at 180iterations finished qdiffx linear iterations at : 07:54:49 total time elapsed so far: 11.05000 # loops : 180 mean,max change (kT/e) : 7.6792995E-04 1.4671326E-02 energy calculations done at 11.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.21000 DelPhi exited at 07:54:50 11.215u 0.180s 0:12.14 93.8% 0+0k 0+0io 0pf+0w