Tue Oct 11 00:58:59 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+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 Tue Oct 11 2011 at 00:58:59 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2784 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 !!! WARNING: LEU 299 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6409333 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): -15.56100 34.80000 ymin,ymax (A): -25.84400 27.22900 zmin,zma (A): -22.77500 32.76900 x,y,z range (A): 50.36100 53.07300 55.54400 scale (grids/A): 0.6409333 object centre (A): 9.619501 0.6925001 4.997001 number of atom coordinates read : 2784 total number of charged atoms : 2630 net assigned charge : 4.040017 assigned positive charge : 422.2776 centred at (gu) : 88.77551 89.17048 89.61233 assigned negative charge : -418.2381 centred at (gu) : 88.71744 89.19272 89.84286 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7590 nv = 96 ne = 84 npr = 56603 no. pairs analyzed = 56603 no. exposed pairs = 3245 no. arc points = 23188 no. surface atoms = 1101 nbur = 1683 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 395 mr = 4273 m= 2 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 112 time to turn everything in is 0.3300000 number of dielectric boundary points 3649 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2321 ## 224 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9193 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8002071E-08 -2.2404475E-08 midg,1,midg; midg,igrid,midg 1.0566939E-08 2.6777154E-09 1,midg,midg; igrid,midg,midg -2.0852893E-09 1.0379124E-08 gauss-seidel spectral radius is 0.9874017 estimated iterations to convergence 73 setup time was (sec) 0.5800000 now iterating at: 00:59:00 rms-change max change #iterations 0.1595562 23.88319 at 10iterations 1.6255762E-02 2.387653 at 20iterations 2.0398744E-03 0.3383102 at 30iterations 4.0101752E-04 8.7875366E-02 at 40iterations 1.0720030E-04 2.4894714E-02 at 50iterations finished qdiffx linear iterations at : 00:59:03 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 1.0720030E-04 2.4894714E-02 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 00:59:03 3.594u 0.192s 0:04.12 91.7% 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 Tue Oct 11 2011 at 00:59:03 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2784 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 !!! WARNING: LEU 299 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.922800 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): -15.56100 34.80000 ymin,ymax (A): -25.84400 27.22900 zmin,zma (A): -22.77500 32.76900 x,y,z range (A): 50.36100 53.07300 55.54400 scale (grids/A): 1.922800 object centre (A): 9.619501 0.6925001 4.997001 number of atom coordinates read : 2784 total number of charged atoms : 2630 net assigned charge : 4.040017 assigned positive charge : 422.2776 centred at (gu) : 86.32579 87.51072 88.83612 assigned negative charge : -418.2381 centred at (gu) : 86.15202 87.57796 89.52813 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 82049 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23188 grid for indexing accessible points = 1.400000 m= 29442 mr = 57487 m= 4655 mr = 22154 m= 257 mr = 3027 m= 2 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 4438 time to turn everything in is 0.6400000 number of dielectric boundary points 33633 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 20716 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) : 0.6409333 object centre at (A) : 9.619501 0.6925001 4.997001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9251461E-02 -3.8975928E-02 midg,1,midg; midg,igrid,midg 5.8291235E-04 1.8202975E-02 1,midg,midg; igrid,midg,midg 1.3746819E-02 9.4648851E-03 gauss-seidel spectral radius is 0.9986714 estimated iterations to convergence 217 setup time was (sec) 0.9400000 now iterating at: 00:59:04 rms-change max change #iterations 4.557516 162.2965 at 10iterations 2.150068 72.24045 at 20iterations 1.017287 35.94422 at 30iterations 0.4816138 15.21950 at 40iterations 0.2277628 7.173903 at 50iterations 0.1076648 3.116100 at 60iterations 5.1159389E-02 1.859903 at 70iterations 2.4355320E-02 0.7238302 at 80iterations 1.1593118E-02 0.3710158 at 90iterations 5.5631129E-03 0.1787586 at 100iterations 2.7125056E-03 7.9124451E-02 at 110iterations 1.3546844E-03 5.2852631E-02 at 120iterations finished qdiffx linear iterations at : 00:59:11 total time elapsed so far: 7.970000 # loops : 120 mean,max change (kT/e) : 1.3546844E-03 5.2852631E-02 energy calculations done at 7.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.160000 DelPhi exited at 00:59:12 8.161u 0.231s 0:08.81 95.2% 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 Tue Oct 11 2011 at 00:59:12 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2784 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 !!! WARNING: LEU 299 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.884200 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): -15.56100 34.80000 ymin,ymax (A): -25.84400 27.22900 zmin,zma (A): -22.77500 32.76900 x,y,z range (A): 50.36100 53.07300 55.54400 scale (grids/A): 2.884200 object centre (A): 9.619501 0.6925001 4.997001 number of atom coordinates read : 2784 total number of charged atoms : 2630 net assigned charge : 4.040017 assigned positive charge : 422.2776 centred at (gu) : 84.48876 86.26604 88.25414 assigned negative charge : -418.2381 centred at (gu) : 84.22791 86.36689 89.29217 start vw surface at 0.1700000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 189482 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23188 grid for indexing accessible points = 1.400000 m= 95770 mr = 139016 m= 34869 mr = 79198 m= 8526 mr = 28498 m= 1209 mr = 6559 m= 59 mr = 824 m= 0 mr = 21 time to grow re-entrant surface = 0.8899999 no. cavity mid-points inaccessible to solvent = 14794 time to turn everything in is 1.570000 number of dielectric boundary points 75799 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 21040 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) : 1.922800 object centre at (A) : 9.619501 0.6925001 4.997001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9240742 -0.3653608 midg,1,midg; midg,igrid,midg -4.5914102E-02 0.1294683 1,midg,midg; igrid,midg,midg 0.3835798 8.9111090E-02 gauss-seidel spectral radius is 0.9992623 estimated iterations to convergence 291 setup time was (sec) 1.920000 now iterating at: 00:59:14 rms-change max change #iterations 10.48621 440.2759 at 10iterations 6.090885 154.2065 at 20iterations 3.527215 85.05894 at 30iterations 2.040483 35.50826 at 40iterations 1.175408 19.96445 at 50iterations 0.6778859 11.70768 at 60iterations 0.3897290 6.795576 at 70iterations 0.2246179 3.893902 at 80iterations 0.1290972 2.286451 at 90iterations 7.4472800E-02 1.261855 at 100iterations 4.2832088E-02 0.7820320 at 110iterations 2.4690980E-02 0.4569550 at 120iterations 1.4246743E-02 0.2449532 at 130iterations 8.2665626E-03 0.1345482 at 140iterations 4.8121111E-03 8.5517883E-02 at 150iterations 2.8479861E-03 6.1265945E-02 at 160iterations 1.7163049E-03 3.6315918E-02 at 170iterations 1.0748754E-03 2.3811340E-02 at 180iterations finished qdiffx linear iterations at : 00:59:25 total time elapsed so far: 13.12000 # loops : 180 mean,max change (kT/e) : 1.0748754E-03 2.3811340E-02 energy calculations done at 13.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.32000 DelPhi exited at 00:59:26 13.324u 0.238s 0:13.91 97.4% 0+0k 0+0io 0pf+0w