Mon Oct 10 09:09:46 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 09:09:46 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 = 1968 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: 0.6325628 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): -35.13500 10.44200 ymin,ymax (A): 1.597000 42.40600 zmin,zma (A): -0.1940000 56.08500 x,y,z range (A): 45.57700 40.80900 56.27900 scale (grids/A): 0.6325628 object centre (A): -12.34650 22.00150 27.94550 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 3.000004 assigned positive charge : 287.8720 centred at (gu) : 90.25880 89.11867 89.97309 assigned negative charge : -284.8723 centred at (gu) : 90.18256 89.26499 89.97094 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5346 nv = 96 ne = 84 npr = 40514 no. pairs analyzed = 40514 no. exposed pairs = 2420 no. arc points = 16861 no. surface atoms = 824 nbur = 1144 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 314 mr = 3024 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 2587 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1667 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6384 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2794045E-09 3.5413839E-09 midg,1,midg; midg,igrid,midg 1.6314402E-08 -5.7067093E-09 1,midg,midg; igrid,midg,midg -1.8331140E-09 9.1841521E-09 gauss-seidel spectral radius is 0.9869986 estimated iterations to convergence 72 setup time was (sec) 0.3600000 now iterating at: 09:09:46 rms-change max change #iterations 0.1151409 18.79175 at 10iterations 1.1240381E-02 2.020985 at 20iterations 1.0654548E-03 0.1739264 at 30iterations 1.0291189E-04 1.7333984E-02 at 40iterations 9.6951326E-06 1.5258789E-03 at 50iterations finished qdiffx linear iterations at : 09:09:49 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 9.6951326E-06 1.5258789E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 09:09:50 3.400u 0.170s 0:03.87 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 09:09:50 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 = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.897688 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): -35.13500 10.44200 ymin,ymax (A): 1.597000 42.40600 zmin,zma (A): -0.1940000 56.08500 x,y,z range (A): 45.57700 40.80900 56.27900 scale (grids/A): 1.897688 object centre (A): -12.34650 22.00150 27.94550 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 3.000004 assigned positive charge : 287.8720 centred at (gu) : 90.77638 87.35610 89.91926 assigned negative charge : -284.8723 centred at (gu) : 90.54814 87.79504 89.91302 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 57346 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16861 grid for indexing accessible points = 1.400000 m= 21799 mr = 39735 m= 3607 mr = 16757 m= 212 mr = 2485 m= 1 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 104 time to turn everything in is 0.2900000 number of dielectric boundary points 23912 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 14449 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) : 0.6325628 object centre at (A) : -12.34650 22.00150 27.94550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6294515E-02 3.4476377E-02 midg,1,midg; midg,igrid,midg 4.2261630E-03 -7.2633331E-03 1,midg,midg; igrid,midg,midg -4.3263859E-03 -3.9512645E-03 gauss-seidel spectral radius is 0.9985498 estimated iterations to convergence 208 setup time was (sec) 0.5000000 now iterating at: 09:09:51 rms-change max change #iterations 3.501164 181.2667 at 10iterations 1.603917 59.49921 at 20iterations 0.7371664 26.01799 at 30iterations 0.3371773 12.45998 at 40iterations 0.1543920 5.233357 at 50iterations 7.0418879E-02 2.362812 at 60iterations 3.2217700E-02 1.143541 at 70iterations 1.4797093E-02 0.5435215 at 80iterations 6.7422395E-03 0.2334247 at 90iterations 3.0802733E-03 0.1242199 at 100iterations 1.4145134E-03 4.8418999E-02 at 110iterations 6.4792775E-04 2.2206306E-02 at 120iterations finished qdiffx linear iterations at : 09:09:58 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 6.4792775E-04 2.2206306E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 09:09:58 7.734u 0.221s 0:08.28 96.0% 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 Mon Oct 10 2011 at 09:09:58 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 = 1968 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: 2.846532 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): -35.13500 10.44200 ymin,ymax (A): 1.597000 42.40600 zmin,zma (A): -0.1940000 56.08500 x,y,z range (A): 45.57700 40.80900 56.27900 scale (grids/A): 2.846532 object centre (A): -12.34650 22.00150 27.94550 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 3.000004 assigned positive charge : 287.8720 centred at (gu) : 91.16450 86.03412 89.87899 assigned negative charge : -284.8723 centred at (gu) : 90.82211 86.69267 89.86955 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 132098 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16861 grid for indexing accessible points = 1.400000 m= 69160 mr = 95586 m= 26760 mr = 57813 m= 6710 mr = 22422 m= 924 mr = 5308 m= 71 mr = 647 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 350 time to turn everything in is 0.7800000 number of dielectric boundary points 53908 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 14687 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) : 1.897688 object centre at (A) : -12.34650 22.00150 27.94550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4503851E-02 0.2222530 midg,1,midg; midg,igrid,midg -3.9391343E-02 -0.1028469 1,midg,midg; igrid,midg,midg -8.5571274E-02 -7.9169340E-02 gauss-seidel spectral radius is 0.9992189 estimated iterations to convergence 282 setup time was (sec) 1.010000 now iterating at: 09:09:59 rms-change max change #iterations 8.231205 391.8478 at 10iterations 4.687600 107.0596 at 20iterations 2.642589 52.72132 at 30iterations 1.498008 33.91164 at 40iterations 0.8434203 16.42050 at 50iterations 0.4779274 11.37555 at 60iterations 0.2691480 6.214525 at 70iterations 0.1520946 2.952132 at 80iterations 8.5976683E-02 1.660317 at 90iterations 4.8563022E-02 1.060024 at 100iterations 2.7449537E-02 0.5835152 at 110iterations 1.5530536E-02 0.3356724 at 120iterations 8.7553943E-03 0.1832390 at 130iterations 4.9319919E-03 0.1017570 at 140iterations 2.7875302E-03 5.9047699E-02 at 150iterations 1.5761754E-03 3.2134533E-02 at 160iterations 8.8973390E-04 1.6674995E-02 at 170iterations 5.0278858E-04 9.8514557E-03 at 180iterations finished qdiffx linear iterations at : 09:10:10 total time elapsed so far: 12.03000 # loops : 180 mean,max change (kT/e) : 5.0278858E-04 9.8514557E-03 energy calculations done at 12.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.16000 DelPhi exited at 09:10:11 12.166u 0.193s 0:12.63 97.7% 0+0k 0+0io 0pf+0w