Sun Oct 9 07:35:59 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 Sun Oct 9 2011 at 07:35:59 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 = 1697 !!! WARNING: NAP 164 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: 0.6984227 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): -8.198000 33.76400 ymin,ymax (A): 2.226000 43.06600 zmin,zma (A): 9.329000 60.30100 x,y,z range (A): 41.96200 40.84000 50.97200 scale (grids/A): 0.6984227 object centre (A): 12.78300 22.64600 34.81500 number of atom coordinates read : 1697 total number of charged atoms : 1560 net assigned charge : -11.49999 assigned positive charge : 251.0242 centred at (gu) : 91.61347 89.48982 89.54214 assigned negative charge : -262.5241 centred at (gu) : 91.39935 89.68330 89.78236 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5545 nv = 96 ne = 84 npr = 36900 no. pairs analyzed = 36900 no. exposed pairs = 2053 no. arc points = 14551 no. surface atoms = 698 nbur = 999 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 340 mr = 3125 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.2300000 number of dielectric boundary points 2708 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1292 ## 85 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6148 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2310815E-11 -1.4918639E-07 midg,1,midg; midg,igrid,midg -1.6695655E-08 -1.3274554E-07 1,midg,midg; igrid,midg,midg -1.1252369E-07 -1.0193314E-08 gauss-seidel spectral radius is 0.9892810 estimated iterations to convergence 79 setup time was (sec) 0.4600000 now iterating at: 07:36:00 rms-change max change #iterations 0.1788413 35.30539 at 10iterations 2.1170802E-02 3.314875 at 20iterations 2.5409653E-03 0.4173126 at 30iterations 2.9856426E-04 4.1212082E-02 at 40iterations 3.5634133E-05 5.1116943E-03 at 50iterations finished qdiffx linear iterations at : 07:36:02 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 3.5634133E-05 5.1116943E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 07:36:03 3.129u 0.186s 0:03.60 91.6% 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 Sun Oct 9 2011 at 07:36:03 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 = 1697 !!! WARNING: NAP 164 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: 2.095268 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): -8.198000 33.76400 ymin,ymax (A): 2.226000 43.06600 zmin,zma (A): 9.329000 60.30100 x,y,z range (A): 41.96200 40.84000 50.97200 scale (grids/A): 2.095268 object centre (A): 12.78300 22.64600 34.81500 number of atom coordinates read : 1697 total number of charged atoms : 1560 net assigned charge : -11.49999 assigned positive charge : 251.0242 centred at (gu) : 94.84061 88.46962 88.62642 assigned negative charge : -262.5241 centred at (gu) : 94.19822 89.05001 89.34734 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 57998 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14551 grid for indexing accessible points = 1.400000 m= 23009 mr = 39920 m= 4338 mr = 17813 m= 347 mr = 2933 m= 8 mr = 162 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 716 time to turn everything in is 0.4400000 number of dielectric boundary points 24870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 12408 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) : 0.6984227 object centre at (A) : 12.78300 22.64600 34.81500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1518767E-02 -8.4917866E-02 midg,1,midg; midg,igrid,midg -1.0542744E-02 -4.7802940E-02 1,midg,midg; igrid,midg,midg -6.4527094E-02 -6.2853741E-03 gauss-seidel spectral radius is 0.9987642 estimated iterations to convergence 225 setup time was (sec) 0.7200000 now iterating at: 07:36:04 rms-change max change #iterations 4.127618 195.2941 at 10iterations 2.006104 71.23486 at 20iterations 0.9744871 38.99860 at 30iterations 0.4764567 17.12536 at 40iterations 0.2311685 8.525882 at 50iterations 0.1119649 3.706398 at 60iterations 5.4434836E-02 1.799739 at 70iterations 2.6532894E-02 0.9232922 at 80iterations 1.2899242E-02 0.4766998 at 90iterations 6.2954663E-03 0.2141376 at 100iterations 3.0664813E-03 0.1019592 at 110iterations 1.4807063E-03 4.8202515E-02 at 120iterations finished qdiffx linear iterations at : 07:36:10 total time elapsed so far: 7.350000 # loops : 120 mean,max change (kT/e) : 1.4807063E-03 4.8202515E-02 energy calculations done at 7.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.520000 DelPhi exited at 07:36:11 7.523u 0.223s 0:08.02 96.5% 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 07:36:11 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 = 1697 !!! WARNING: NAP 164 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.142902 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): -8.198000 33.76400 ymin,ymax (A): 2.226000 43.06600 zmin,zma (A): 9.329000 60.30100 x,y,z range (A): 41.96200 40.84000 50.97200 scale (grids/A): 3.142902 object centre (A): 12.78300 22.64600 34.81500 number of atom coordinates read : 1697 total number of charged atoms : 1560 net assigned charge : -11.49999 assigned positive charge : 251.0242 centred at (gu) : 97.26093 87.70450 87.93974 assigned negative charge : -262.5241 centred at (gu) : 96.29732 88.57508 89.02094 start vw surface at 0.1200000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 133614 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14551 grid for indexing accessible points = 1.400000 m= 71205 mr = 96284 m= 29828 mr = 59515 m= 8081 mr = 24959 m= 1368 mr = 6291 m= 147 mr = 939 m= 8 mr = 109 m= 0 mr = 2 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 2362 time to turn everything in is 1.360000 number of dielectric boundary points 56152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 12480 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) : 2.095268 object centre at (A) : 12.78300 22.64600 34.81500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1137695 -0.7153663 midg,1,midg; midg,igrid,midg -0.1196038 -0.3624738 1,midg,midg; igrid,midg,midg -0.5669150 -4.7712818E-02 gauss-seidel spectral radius is 0.9992716 estimated iterations to convergence 292 setup time was (sec) 1.660000 now iterating at: 07:36:13 rms-change max change #iterations 9.212572 431.4930 at 10iterations 5.288393 129.7083 at 20iterations 3.057183 64.17009 at 30iterations 1.761222 38.71769 at 40iterations 1.018452 24.60784 at 50iterations 0.5869474 11.61779 at 60iterations 0.3385836 6.404950 at 70iterations 0.1952897 3.966724 at 80iterations 0.1127192 2.046145 at 90iterations 6.4920604E-02 1.222637 at 100iterations 3.7361506E-02 0.7074413 at 110iterations 2.1521911E-02 0.4210545 at 120iterations 1.2453619E-02 0.2393026 at 130iterations 7.1686106E-03 0.1350155 at 140iterations 4.1217259E-03 8.1412315E-02 at 150iterations 2.3832505E-03 4.4952393E-02 at 160iterations 1.3747788E-03 2.6377678E-02 at 170iterations 7.9042814E-04 1.6777039E-02 at 180iterations finished qdiffx linear iterations at : 07:36:23 total time elapsed so far: 12.21000 # loops : 180 mean,max change (kT/e) : 7.9042814E-04 1.6777039E-02 energy calculations done at 12.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.39000 DelPhi exited at 07:36:24 12.396u 0.235s 0:13.00 97.0% 0+0k 0+0io 0pf+0w