Mon Oct 10 11:34:04 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 Mon Oct 10 2011 at 11:34:04 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2136 !!! WARNING: ASL 51 has a net charge of -0.1000 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: 0.6710650 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): -22.23400 24.90900 ymin,ymax (A): -21.14400 26.40700 zmin,zma (A): -16.75600 36.29400 x,y,z range (A): 47.14300 47.55100 53.05000 scale (grids/A): 0.6710650 object centre (A): 1.337501 2.631500 9.768999 number of atom coordinates read : 2136 total number of charged atoms : 1995 net assigned charge : -8.099972 assigned positive charge : 322.4319 centred at (gu) : 91.98048 88.65323 92.17633 assigned negative charge : -330.5320 centred at (gu) : 92.09284 88.59802 91.92802 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6364 nv = 96 ne = 84 npr = 44704 no. pairs analyzed = 44704 no. exposed pairs = 2682 no. arc points = 18879 no. surface atoms = 902 nbur = 1234 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 354 mr = 3439 m= 0 mr = 44 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3200000 number of dielectric boundary points 3235 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1691 ## 130 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7320 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4006527E-08 4.1445801E-08 midg,1,midg; midg,igrid,midg -5.2658230E-08 -1.2242329E-08 1,midg,midg; igrid,midg,midg -2.6670499E-09 -7.9471803E-08 gauss-seidel spectral radius is 0.9884442 estimated iterations to convergence 76 setup time was (sec) 0.5300000 now iterating at: 11:34:04 rms-change max change #iterations 0.1656309 31.81605 at 10iterations 1.8399078E-02 2.438781 at 20iterations 1.9934727E-03 0.2807007 at 30iterations 2.1491868E-04 3.1642914E-02 at 40iterations 2.3937841E-05 3.3502579E-03 at 50iterations finished qdiffx linear iterations at : 11:34:07 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 2.3937841E-05 3.3502579E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 11:34:08 3.518u 0.173s 0:03.99 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 Mon Oct 10 2011 at 11:34:08 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2136 !!! WARNING: ASL 51 has a net charge of -0.1000 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: 2.013195 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): -22.23400 24.90900 ymin,ymax (A): -21.14400 26.40700 zmin,zma (A): -16.75600 36.29400 x,y,z range (A): 47.14300 47.55100 53.05000 scale (grids/A): 2.013195 object centre (A): 1.337501 2.631500 9.768999 number of atom coordinates read : 2136 total number of charged atoms : 1995 net assigned charge : -8.099972 assigned positive charge : 322.4319 centred at (gu) : 95.94141 85.95969 96.52885 assigned negative charge : -330.5320 centred at (gu) : 96.27872 85.79407 95.78404 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 67470 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18879 grid for indexing accessible points = 1.400000 m= 24067 mr = 45852 m= 3958 mr = 17501 m= 258 mr = 2509 m= 7 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1016 time to turn everything in is 0.5300000 number of dielectric boundary points 29802 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 15772 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) : 0.6710650 object centre at (A) : 1.337501 2.631500 9.768999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5295991E-02 -3.5818690E-03 midg,1,midg; midg,igrid,midg -1.4591057E-02 1.2695823E-03 1,midg,midg; igrid,midg,midg -1.0792363E-02 -5.3090535E-02 gauss-seidel spectral radius is 0.9987191 estimated iterations to convergence 221 setup time was (sec) 0.8100000 now iterating at: 11:34:09 rms-change max change #iterations 4.269627 222.5694 at 10iterations 2.053404 80.16367 at 20iterations 0.9772559 35.85606 at 30iterations 0.4694250 15.91760 at 40iterations 0.2243694 7.274441 at 50iterations 0.1074541 3.721535 at 60iterations 5.1654588E-02 1.891457 at 70iterations 2.4727525E-02 0.8280411 at 80iterations 1.1847779E-02 0.3981800 at 90iterations 5.6832354E-03 0.1945763 at 100iterations 2.7185695E-03 8.9570999E-02 at 110iterations 1.3077520E-03 4.1547775E-02 at 120iterations finished qdiffx linear iterations at : 11:34:15 total time elapsed so far: 7.280000 # loops : 120 mean,max change (kT/e) : 1.3077520E-03 4.1547775E-02 energy calculations done at 7.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.500000 DelPhi exited at 11:34:16 7.507u 0.186s 0:08.02 95.7% 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 11:34:16 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2136 !!! WARNING: ASL 51 has a net charge of -0.1000 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: 3.019793 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): -22.23400 24.90900 ymin,ymax (A): -21.14400 26.40700 zmin,zma (A): -16.75600 36.29400 x,y,z range (A): 47.14300 47.55100 53.05000 scale (grids/A): 3.019793 object centre (A): 1.337501 2.631500 9.768999 number of atom coordinates read : 2136 total number of charged atoms : 1995 net assigned charge : -8.099972 assigned positive charge : 322.4319 centred at (gu) : 98.91195 83.93949 99.79322 assigned negative charge : -330.5320 centred at (gu) : 99.41803 83.69105 98.67597 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 155900 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18879 grid for indexing accessible points = 1.400000 m= 77487 mr = 111064 m= 28179 mr = 62954 m= 7226 mr = 22484 m= 1169 mr = 5473 m= 112 mr = 798 m= 1 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 3612 time to turn everything in is 1.360000 number of dielectric boundary points 67241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 15960 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) : 2.013195 object centre at (A) : 1.337501 2.631500 9.768999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3233089 6.7092232E-02 midg,1,midg; midg,igrid,midg -7.9550140E-02 -1.0151487E-02 1,midg,midg; igrid,midg,midg -0.1362456 -0.4574770 gauss-seidel spectral radius is 0.9992760 estimated iterations to convergence 293 setup time was (sec) 1.680000 now iterating at: 11:34:18 rms-change max change #iterations 9.963760 428.9358 at 10iterations 5.802283 127.1225 at 20iterations 3.372769 73.97606 at 30iterations 1.955167 40.89051 at 40iterations 1.132454 22.92804 at 50iterations 0.6545494 12.79391 at 60iterations 0.3783648 7.568969 at 70iterations 0.2185787 4.152580 at 80iterations 0.1263233 2.548071 at 90iterations 7.2648630E-02 1.289701 at 100iterations 4.2014834E-02 0.7935448 at 110iterations 2.4270002E-02 0.4531143 at 120iterations 1.3989053E-02 0.2743950 at 130iterations 8.1026554E-03 0.1479807 at 140iterations 4.6706330E-03 9.4297886E-02 at 150iterations 2.6937122E-03 4.8706055E-02 at 160iterations 1.5537064E-03 2.7015686E-02 at 170iterations 8.9826144E-04 1.8005371E-02 at 180iterations finished qdiffx linear iterations at : 11:34:29 total time elapsed so far: 12.71000 # loops : 180 mean,max change (kT/e) : 8.9826144E-04 1.8005371E-02 energy calculations done at 12.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 11:34:29 12.900u 0.205s 0:13.42 97.6% 0+0k 0+0io 0pf+0w