Mon Oct 10 09:13:50 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 09:13:50 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 = 1964 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: 0.6469551 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): -6.185000 34.43400 ymin,ymax (A): -3.521000 47.90800 zmin,zma (A): -24.11200 30.91500 x,y,z range (A): 40.61900 51.42900 55.02700 scale (grids/A): 0.6469551 object centre (A): 14.12450 22.19350 3.401501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 90.94885 92.60786 90.13832 assigned negative charge : -284.8263 centred at (gu) : 91.05116 92.73866 90.09633 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5560 nv = 96 ne = 84 npr = 40561 no. pairs analyzed = 40561 no. exposed pairs = 2437 no. arc points = 17025 no. surface atoms = 826 nbur = 1138 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 290 mr = 3130 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 40 time to turn everything in is 0.2500000 number of dielectric boundary points 2680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1659 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6539 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4425057E-09 1.0362565E-08 midg,1,midg; midg,igrid,midg 1.0992861E-08 -1.4094083E-08 1,midg,midg; igrid,midg,midg 1.3210415E-08 -5.9583445E-09 gauss-seidel spectral radius is 0.9875614 estimated iterations to convergence 73 setup time was (sec) 0.4800000 now iterating at: 09:13:51 rms-change max change #iterations 0.1314467 21.11299 at 10iterations 1.3256159E-02 1.980522 at 20iterations 1.3270950E-03 0.2301273 at 30iterations 1.3519172E-04 2.2872925E-02 at 40iterations 1.3446315E-05 2.1610260E-03 at 50iterations finished qdiffx linear iterations at : 09:13:54 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 1.3446315E-05 2.1610260E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 09:13:54 3.513u 0.155s 0:03.93 93.1% 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 09:13:54 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 = 1964 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: 1.940865 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): -6.185000 34.43400 ymin,ymax (A): -3.521000 47.90800 zmin,zma (A): -24.11200 30.91500 x,y,z range (A): 40.61900 51.42900 55.02700 scale (grids/A): 1.940865 object centre (A): 14.12450 22.19350 3.401501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 92.84646 97.82355 90.41507 assigned negative charge : -284.8263 centred at (gu) : 93.15366 98.21600 90.28917 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 59949 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17025 grid for indexing accessible points = 1.400000 m= 21838 mr = 41659 m= 3375 mr = 16612 m= 168 mr = 2252 m= 3 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1432 time to turn everything in is 0.4700000 number of dielectric boundary points 24751 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 14457 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) : 0.6469551 object centre at (A) : 14.12450 22.19350 3.401501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7372583E-02 1.6799778E-02 midg,1,midg; midg,igrid,midg 3.4996048E-02 -7.4411165E-03 1,midg,midg; igrid,midg,midg 8.9058680E-03 -5.7590683E-03 gauss-seidel spectral radius is 0.9986037 estimated iterations to convergence 212 setup time was (sec) 0.7600000 now iterating at: 09:13:55 rms-change max change #iterations 3.675207 154.3897 at 10iterations 1.712730 68.27928 at 20iterations 0.7962575 28.64950 at 30iterations 0.3693906 12.36099 at 40iterations 0.1717697 6.139542 at 50iterations 7.9411723E-02 2.763660 at 60iterations 3.6819920E-02 1.353230 at 70iterations 1.7152449E-02 0.6151609 at 80iterations 7.9395343E-03 0.2776699 at 90iterations 3.7008070E-03 0.1281734 at 100iterations 1.7058763E-03 5.7285309E-02 at 110iterations 7.9464231E-04 3.1502724E-02 at 120iterations finished qdiffx linear iterations at : 09:14:02 total time elapsed so far: 7.190000 # loops : 120 mean,max change (kT/e) : 7.9464231E-04 3.1502724E-02 energy calculations done at 7.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.380000 DelPhi exited at 09:14:02 7.382u 0.172s 0:07.88 95.8% 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 09:14:02 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.911298 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): -6.185000 34.43400 ymin,ymax (A): -3.521000 47.90800 zmin,zma (A): -24.11200 30.91500 x,y,z range (A): 40.61900 51.42900 55.02700 scale (grids/A): 2.911298 object centre (A): 14.12450 22.19350 3.401501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 94.26976 101.7352 90.62269 assigned negative charge : -284.8263 centred at (gu) : 94.73063 102.3240 90.43379 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 138536 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17025 grid for indexing accessible points = 1.400000 m= 70393 mr = 100489 m= 25733 mr = 58585 m= 6058 mr = 21409 m= 801 mr = 4709 m= 33 mr = 554 m= 0 mr = 13 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 4555 time to turn everything in is 1.150000 number of dielectric boundary points 55795 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 14656 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) : 1.940865 object centre at (A) : 14.12450 22.19350 3.401501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.033165 4.1486863E-02 midg,1,midg; midg,igrid,midg 0.3502198 -0.1093845 1,midg,midg; igrid,midg,midg 5.8357123E-02 -3.5235878E-02 gauss-seidel spectral radius is 0.9992361 estimated iterations to convergence 286 setup time was (sec) 1.460000 now iterating at: 09:14:04 rms-change max change #iterations 8.532156 384.0182 at 10iterations 4.892601 116.8130 at 20iterations 2.775453 61.45416 at 30iterations 1.577851 33.46264 at 40iterations 0.8975924 20.72831 at 50iterations 0.5096000 11.71679 at 60iterations 0.2899019 5.755096 at 70iterations 0.1644842 3.396706 at 80iterations 9.3352407E-02 1.703108 at 90iterations 5.3053088E-02 0.9778609 at 100iterations 3.0109392E-02 0.5786667 at 110iterations 1.7081268E-02 0.3217528 at 120iterations 9.7121298E-03 0.1996040 at 130iterations 5.5098720E-03 0.1173859 at 140iterations 3.1382621E-03 6.1523438E-02 at 150iterations 1.7817949E-03 3.7035942E-02 at 160iterations 1.0126096E-03 1.9907951E-02 at 170iterations 5.7508203E-04 1.2092590E-02 at 180iterations finished qdiffx linear iterations at : 09:14:14 total time elapsed so far: 11.73000 # loops : 180 mean,max change (kT/e) : 5.7508203E-04 1.2092590E-02 energy calculations done at 11.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.93000 DelPhi exited at 09:14:15 11.929u 0.228s 0:12.51 97.0% 0+0k 0+0io 0pf+0w