Wed Dec 21 14:21:38 PST 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 Wed Dec 21 2011 at 14:21:39 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: 252 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: 0.6453250 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): -5.525000 35.07100 ymin,ymax (A): -3.494000 47.94500 zmin,zma (A): -24.28900 30.87700 x,y,z range (A): 40.59600 51.43900 55.16600 scale (grids/A): 0.6453250 object centre (A): 14.77300 22.22550 3.294001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 90.64860 92.77505 90.22300 assigned negative charge : -285.8263 centred at (gu) : 90.78618 92.95532 90.15892 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5612 nv = 96 ne = 84 npr = 40063 no. pairs analyzed = 40063 no. exposed pairs = 2421 no. arc points = 16837 no. surface atoms = 818 nbur = 1146 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 278 mr = 3214 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 48 time to turn everything in is 0.3300000 number of dielectric boundary points 2631 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1715 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 6588 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1922082E-09 1.0768924E-08 midg,1,midg; midg,igrid,midg 1.1903698E-08 -2.6081008E-08 1,midg,midg; igrid,midg,midg 1.5089132E-08 -1.1181628E-08 gauss-seidel spectral radius is 0.9875003 estimated iterations to convergence 73 setup time was (sec) 0.6500000 now iterating at: 14:21:41 rms-change max change #iterations 0.1216658 21.69961 at 10iterations 1.2770080E-02 1.791355 at 20iterations 1.2587259E-03 0.1801021 at 30iterations 1.2742849E-04 2.7347565E-02 at 40iterations 1.2519305E-05 2.0837784E-03 at 50iterations finished qdiffx linear iterations at : 14:21:47 total time elapsed so far: 6.180000 # loops : 50 mean,max change (kT/e) : 1.2519305E-05 2.0837784E-03 energy calculations done at 6.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.410000 DelPhi exited at 14:21:58 6.410u 0.579s 0:19.68 35.4% 0+0k 0+0io 6pf+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 Wed Dec 21 2011 at 14:22:00 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: 252 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: 1.935975 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): -5.525000 35.07100 ymin,ymax (A): -3.494000 47.94500 zmin,zma (A): -24.28900 30.87700 x,y,z range (A): 40.59600 51.43900 55.16600 scale (grids/A): 1.935975 object centre (A): 14.77300 22.22550 3.294001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 91.94580 98.32529 90.66894 assigned negative charge : -285.8263 centred at (gu) : 92.35859 98.86600 90.47674 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 60226 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16837 grid for indexing accessible points = 1.400000 m= 22602 mr = 42167 m= 3384 mr = 17528 m= 197 mr = 2243 m= 5 mr = 104 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1319 time to turn everything in is 0.6100000 number of dielectric boundary points 24373 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 14472 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) : 0.6453250 object centre at (A) : 14.77300 22.22550 3.294001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3631092E-02 1.4529267E-02 midg,1,midg; midg,igrid,midg 3.4127541E-02 -2.0533020E-02 1,midg,midg; igrid,midg,midg 1.0269086E-02 -7.1266871E-03 gauss-seidel spectral radius is 0.9985966 estimated iterations to convergence 212 setup time was (sec) 0.9400000 now iterating at: 14:22:01 rms-change max change #iterations 3.667038 197.6852 at 10iterations 1.696327 63.70665 at 20iterations 0.7902675 29.87923 at 30iterations 0.3665332 13.47528 at 40iterations 0.1695880 5.912018 at 50iterations 7.8581356E-02 2.893553 at 60iterations 3.6431003E-02 1.203202 at 70iterations 1.6857456E-02 0.6048473 at 80iterations 7.8189876E-03 0.2630520 at 90iterations 3.6385839E-03 0.1245880 at 100iterations 1.6783837E-03 5.6613922E-02 at 110iterations 7.7985541E-04 2.7927399E-02 at 120iterations finished qdiffx linear iterations at : 14:22:16 total time elapsed so far: 15.82000 # loops : 120 mean,max change (kT/e) : 7.7985541E-04 2.7927399E-02 energy calculations done at 15.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.03000 DelPhi exited at 14:22:25 16.035u 0.526s 0:25.43 65.0% 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 Wed Dec 21 2011 at 14:22:26 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: 252 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: 2.903963 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): -5.525000 35.07100 ymin,ymax (A): -3.494000 47.94500 zmin,zma (A): -24.28900 30.87700 x,y,z range (A): 40.59600 51.43900 55.16600 scale (grids/A): 2.903963 object centre (A): 14.77300 22.22550 3.294001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 92.91868 102.4881 91.00347 assigned negative charge : -285.8263 centred at (gu) : 93.53784 103.2991 90.71516 start vw surface at 0.1500000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 139272 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16837 grid for indexing accessible points = 1.400000 m= 72730 mr = 101727 m= 26685 mr = 61052 m= 5924 mr = 22363 m= 845 mr = 4697 m= 71 mr = 642 m= 0 mr = 42 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 4418 time to turn everything in is 1.640000 number of dielectric boundary points 55004 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.790000 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) : 1.935975 object centre at (A) : 14.77300 22.22550 3.294001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.019691 -2.2922639E-02 midg,1,midg; midg,igrid,midg 0.3783343 -0.2131225 1,midg,midg; igrid,midg,midg 6.7759641E-02 -4.8419528E-02 gauss-seidel spectral radius is 0.9992335 estimated iterations to convergence 285 setup time was (sec) 2.010000 now iterating at: 14:22:29 rms-change max change #iterations 8.567052 360.2904 at 10iterations 4.913894 120.7425 at 20iterations 2.788807 54.40977 at 30iterations 1.583366 33.28711 at 40iterations 0.9007869 19.94699 at 50iterations 0.5111606 10.37731 at 60iterations 0.2900959 5.606900 at 70iterations 0.1648678 3.478416 at 80iterations 9.3284279E-02 1.832195 at 90iterations 5.3007923E-02 1.138610 at 100iterations 3.0081768E-02 0.6738788 at 110iterations 1.7083393E-02 0.3403244 at 120iterations 9.6868770E-03 0.1956589 at 130iterations 5.5046184E-03 0.1183949 at 140iterations 3.1270876E-03 5.8857441E-02 at 150iterations 1.7740986E-03 3.6958694E-02 at 160iterations 1.0094275E-03 2.0368576E-02 at 170iterations 5.7288248E-04 1.2222290E-02 at 180iterations finished qdiffx linear iterations at : 14:22:56 total time elapsed so far: 28.13000 # loops : 180 mean,max change (kT/e) : 5.7288248E-04 1.2222290E-02 energy calculations done at 28.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 28.36000 DelPhi exited at 14:23:00 28.363u 0.565s 0:33.50 86.3% 0+0k 0+0io 0pf+0w