Mon Oct 10 14:03:02 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 Mon Oct 10 2011 at 14:03:02 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2011 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NAP 187 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7159808 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): -25.12000 22.03700 ymin,ymax (A): -23.83400 25.88800 zmin,zma (A): -14.29700 35.40200 x,y,z range (A): 47.15700 49.72200 49.69900 scale (grids/A): 0.7159808 object centre (A): -1.541499 1.027000 10.55250 number of atom coordinates read : 2011 total number of charged atoms : 1871 net assigned charge : 1.5750527E-05 assigned positive charge : 302.2679 centred at (gu) : 90.32993 89.74102 90.11752 assigned negative charge : -302.2682 centred at (gu) : 90.19150 89.75785 90.17540 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7093 nv = 96 ne = 84 npr = 41688 no. pairs analyzed = 41688 no. exposed pairs = 2472 no. arc points = 17830 no. surface atoms = 838 nbur = 1173 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 497 mr = 3966 m= 2 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.2400000 number of dielectric boundary points 3522 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1565 ## 125 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 7639 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2330306E-08 -3.4689009E-08 midg,1,midg; midg,igrid,midg 1.0012327E-08 -9.4666595E-09 1,midg,midg; igrid,midg,midg -7.6270396E-08 8.4111456E-08 gauss-seidel spectral radius is 0.9898297 estimated iterations to convergence 81 setup time was (sec) 0.4700000 now iterating at: 14:03:02 rms-change max change #iterations 0.2082429 28.76611 at 10iterations 2.6161175E-02 3.573349 at 20iterations 3.3024985E-03 0.4447632 at 30iterations 4.1036308E-04 5.6360245E-02 at 40iterations 5.1745636E-05 7.0075989E-03 at 50iterations finished qdiffx linear iterations at : 14:03:05 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 5.1745636E-05 7.0075989E-03 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 14:03:06 3.312u 0.210s 0:04.11 85.6% 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 Mon Oct 10 2011 at 14:03:06 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2011 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NAP 187 has a net charge of -2.0000 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: 2.147943 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): -25.12000 22.03700 ymin,ymax (A): -23.83400 25.88800 zmin,zma (A): -14.29700 35.40200 x,y,z range (A): 47.15700 49.72200 49.69900 scale (grids/A): 2.147943 object centre (A): -1.541499 1.027000 10.55250 number of atom coordinates read : 2011 total number of charged atoms : 1871 net assigned charge : 1.5750527E-05 assigned positive charge : 302.2679 centred at (gu) : 90.98979 89.22316 90.35234 assigned negative charge : -302.2682 centred at (gu) : 90.57454 89.27357 90.52618 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 74496 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17830 grid for indexing accessible points = 1.400000 m= 30072 mr = 51634 m= 6475 mr = 23020 m= 557 mr = 4456 m= 16 mr = 256 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 138 time to turn everything in is 0.6000000 number of dielectric boundary points 32248 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 52 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 14870 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) : 0.7159808 object centre at (A) : -1.541499 1.027000 10.55250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6060602E-03 -5.6907631E-02 midg,1,midg; midg,igrid,midg -3.6777463E-02 1.2482375E-02 1,midg,midg; igrid,midg,midg 3.0664071E-03 4.4521883E-02 gauss-seidel spectral radius is 0.9988570 estimated iterations to convergence 234 setup time was (sec) 0.8900000 now iterating at: 14:03:07 rms-change max change #iterations 4.713838 212.9399 at 10iterations 2.337631 86.10705 at 20iterations 1.170943 35.91283 at 30iterations 0.5818099 19.72372 at 40iterations 0.2909676 9.286436 at 50iterations 0.1456347 4.402311 at 60iterations 7.2710477E-02 2.397499 at 70iterations 3.6245909E-02 1.093376 at 80iterations 1.8138938E-02 0.6201172 at 90iterations 9.0525467E-03 0.3316031 at 100iterations 4.5107189E-03 0.1380808 at 110iterations 2.2605376E-03 6.9957733E-02 at 120iterations finished qdiffx linear iterations at : 14:03:14 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 2.2605376E-03 6.9957733E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 14:03:14 7.760u 0.223s 0:08.55 93.3% 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 Mon Oct 10 2011 at 14:03:15 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2011 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NAP 187 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.221914 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): -25.12000 22.03700 ymin,ymax (A): -23.83400 25.88800 zmin,zma (A): -14.29700 35.40200 x,y,z range (A): 47.15700 49.72200 49.69900 scale (grids/A): 3.221914 object centre (A): -1.541499 1.027000 10.55250 number of atom coordinates read : 2011 total number of charged atoms : 1871 net assigned charge : 1.5750527E-05 assigned positive charge : 302.2679 centred at (gu) : 91.48466 88.83469 90.52860 assigned negative charge : -302.2682 centred at (gu) : 90.86186 88.91040 90.78934 start vw surface at 0.1300000 fill in re-entrant regions at 0.7800000 boundary points on vw surface= 171758 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17830 grid for indexing accessible points = 1.400000 m= 92593 mr = 124528 m= 39756 mr = 77130 m= 12375 mr = 33185 m= 2456 mr = 9736 m= 258 mr = 1752 m= 14 mr = 143 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 521 time to turn everything in is 1.760000 number of dielectric boundary points 72732 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 14968 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) : 2.147943 object centre at (A) : -1.541499 1.027000 10.55250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0602608E-02 -0.5025565 midg,1,midg; midg,igrid,midg -0.5479708 0.2252099 1,midg,midg; igrid,midg,midg 3.1173786E-02 0.2696249 gauss-seidel spectral radius is 0.9993078 estimated iterations to convergence 300 setup time was (sec) 2.070000 now iterating at: 14:03:17 rms-change max change #iterations 10.43673 419.9095 at 10iterations 6.110968 117.4223 at 20iterations 3.587656 74.22959 at 30iterations 2.101977 36.95191 at 40iterations 1.234001 22.86157 at 50iterations 0.7223976 16.10840 at 60iterations 0.4221272 7.141765 at 70iterations 0.2473965 4.665546 at 80iterations 0.1444653 2.421089 at 90iterations 8.4625788E-02 1.580549 at 100iterations 4.9425017E-02 0.8260946 at 110iterations 2.8869299E-02 0.4874666 at 120iterations 1.6884964E-02 0.2804670 at 130iterations 9.8684179E-03 0.1728973 at 140iterations 5.7728412E-03 0.1010170 at 150iterations 3.3755044E-03 6.3964844E-02 at 160iterations 1.9698711E-03 3.4170151E-02 at 170iterations 1.1546910E-03 2.0203590E-02 at 180iterations finished qdiffx linear iterations at : 14:03:27 total time elapsed so far: 12.52000 # loops : 180 mean,max change (kT/e) : 1.1546910E-03 2.0203590E-02 energy calculations done at 12.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.71000 DelPhi exited at 14:03:28 12.708u 0.232s 0:13.41 96.4% 0+0k 0+0io 0pf+0w