Wed Dec 28 11:02:00 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+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 Wed Dec 28 2011 at 11:02:00 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1944 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: GLY 67 has a net charge of 0.2480 !!! WARNING: ASN 82 has a net charge of -0.6880 !!! WARNING: ARG 86 has a net charge of -0.4460 !!! WARNING: ASN 87 has a net charge of -0.6880 !!! WARNING: GLN 91 has a net charge of -0.6880 !!! WARNING: ASN 97 has a net charge of -0.6880 !!! WARNING: GLN 100 has a net charge of -0.6880 !!! WARNING: GLN 105 has a net charge of -0.6880 !!! WARNING: ARG 106 has a net charge of -0.4460 !!! WARNING: GLN 116 has a net charge of -0.6880 !!! WARNING: ARG 139 has a net charge of -0.4460 !!! WARNING: ARG 155 has a net charge of -0.4460 !!! WARNING: GLN 156 has a net charge of -0.6880 !!! WARNING: GLN 159 has a net charge of -0.6880 !!! WARNING: GLY 165 has a net charge of 0.2480 !!! WARNING: ASN 180 has a net charge of -0.6880 !!! WARNING: ARG 184 has a net charge of -0.4460 !!! WARNING: ASN 185 has a net charge of -0.6880 !!! WARNING: GLN 189 has a net charge of -0.6880 !!! WARNING: ASN 195 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6420777 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): -34.93700 10.54600 ymin,ymax (A): 0.4030000 41.32000 zmin,zma (A): -0.7420000 54.70300 x,y,z range (A): 45.48300 40.91700 55.44500 scale (grids/A): 0.6420777 object centre (A): -12.19550 20.86150 26.98050 number of atom coordinates read : 1944 total number of charged atoms : 1744 net assigned charge : -21.45602 assigned positive charge : 265.3884 centred at (gu) : 90.23855 89.71366 90.59362 assigned negative charge : -286.8443 centred at (gu) : 90.13111 89.83701 90.58407 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5531 nv = 96 ne = 84 npr = 40055 no. pairs analyzed = 40055 no. exposed pairs = 2387 no. arc points = 16695 no. surface atoms = 819 nbur = 1125 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 296 mr = 3114 m= 2 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 2681 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1573 ## 118 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6269 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.0162855E-08 -3.6544527E-08 midg,1,midg; midg,igrid,midg -2.3403068E-08 -4.2023675E-08 1,midg,midg; igrid,midg,midg -4.1031022E-08 -2.4670710E-08 gauss-seidel spectral radius is 0.9873738 estimated iterations to convergence 73 setup time was (sec) 0.5300000 now iterating at: 11:02:01 rms-change max change #iterations 0.1373062 26.51532 at 10iterations 1.3785089E-02 2.273455 at 20iterations 1.3402710E-03 0.2403316 at 30iterations 1.3587634E-04 2.1331668E-02 at 40iterations 1.3857953E-05 1.9979477E-03 at 50iterations finished qdiffx linear iterations at : 11:02:07 total time elapsed so far: 6.490000 # loops : 50 mean,max change (kT/e) : 1.3857953E-05 1.9979477E-03 energy calculations done at 6.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.650000 DelPhi exited at 11:02:10 6.656u 0.647s 0:09.77 74.6% 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 28 2011 at 11:02:10 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1944 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: GLY 67 has a net charge of 0.2480 !!! WARNING: ASN 82 has a net charge of -0.6880 !!! WARNING: ARG 86 has a net charge of -0.4460 !!! WARNING: ASN 87 has a net charge of -0.6880 !!! WARNING: GLN 91 has a net charge of -0.6880 !!! WARNING: ASN 97 has a net charge of -0.6880 !!! WARNING: GLN 100 has a net charge of -0.6880 !!! WARNING: GLN 105 has a net charge of -0.6880 !!! WARNING: ARG 106 has a net charge of -0.4460 !!! WARNING: GLN 116 has a net charge of -0.6880 !!! WARNING: ARG 139 has a net charge of -0.4460 !!! WARNING: ARG 155 has a net charge of -0.4460 !!! WARNING: GLN 156 has a net charge of -0.6880 !!! WARNING: GLN 159 has a net charge of -0.6880 !!! WARNING: GLY 165 has a net charge of 0.2480 !!! WARNING: ASN 180 has a net charge of -0.6880 !!! WARNING: ARG 184 has a net charge of -0.4460 !!! WARNING: ASN 185 has a net charge of -0.6880 !!! WARNING: GLN 189 has a net charge of -0.6880 !!! WARNING: ASN 195 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.926233 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): -34.93700 10.54600 ymin,ymax (A): 0.4030000 41.32000 zmin,zma (A): -0.7420000 54.70300 x,y,z range (A): 45.48300 40.91700 55.44500 scale (grids/A): 1.926233 object centre (A): -12.19550 20.86150 26.98050 number of atom coordinates read : 1944 total number of charged atoms : 1744 net assigned charge : -21.45602 assigned positive charge : 265.3884 centred at (gu) : 90.71601 89.14114 91.78111 assigned negative charge : -286.8443 centred at (gu) : 90.39347 89.51110 91.75246 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 58800 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16695 grid for indexing accessible points = 1.400000 m= 22408 mr = 40859 m= 3573 mr = 17168 m= 187 mr = 2280 m= 4 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 62 time to turn everything in is 0.5900000 number of dielectric boundary points 24621 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 80 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 13774 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) : 0.6420777 object centre at (A) : -12.19550 20.86150 26.98050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.6432664E-02 -6.7213804E-02 midg,1,midg; midg,igrid,midg -2.7204294E-02 -4.9216494E-02 1,midg,midg; igrid,midg,midg -2.2887714E-02 -3.8040303E-02 gauss-seidel spectral radius is 0.9985868 estimated iterations to convergence 211 setup time was (sec) 1.140000 now iterating at: 11:02:12 rms-change max change #iterations 3.663692 146.4958 at 10iterations 1.698971 65.14662 at 20iterations 0.7867878 25.66799 at 30iterations 0.3630618 13.46891 at 40iterations 0.1680262 5.471106 at 50iterations 7.7561900E-02 2.942699 at 60iterations 3.5932422E-02 1.345264 at 70iterations 1.6541241E-02 0.6104889 at 80iterations 7.6441830E-03 0.2671900 at 90iterations 3.5324043E-03 0.1419983 at 100iterations 1.6344442E-03 5.9505463E-02 at 110iterations 7.5506308E-04 2.6290894E-02 at 120iterations finished qdiffx linear iterations at : 11:02:31 total time elapsed so far: 20.52000 # loops : 120 mean,max change (kT/e) : 7.5506308E-04 2.6290894E-02 energy calculations done at 20.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.69000 DelPhi exited at 11:02:32 20.697u 0.828s 0:21.87 98.3% 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 28 2011 at 11:02:32 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1944 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: GLY 67 has a net charge of 0.2480 !!! WARNING: ASN 82 has a net charge of -0.6880 !!! WARNING: ARG 86 has a net charge of -0.4460 !!! WARNING: ASN 87 has a net charge of -0.6880 !!! WARNING: GLN 91 has a net charge of -0.6880 !!! WARNING: ASN 97 has a net charge of -0.6880 !!! WARNING: GLN 100 has a net charge of -0.6880 !!! WARNING: GLN 105 has a net charge of -0.6880 !!! WARNING: ARG 106 has a net charge of -0.4460 !!! WARNING: GLN 116 has a net charge of -0.6880 !!! WARNING: ARG 139 has a net charge of -0.4460 !!! WARNING: ARG 155 has a net charge of -0.4460 !!! WARNING: GLN 156 has a net charge of -0.6880 !!! WARNING: GLN 159 has a net charge of -0.6880 !!! WARNING: GLY 165 has a net charge of 0.2480 !!! WARNING: ASN 180 has a net charge of -0.6880 !!! WARNING: ARG 184 has a net charge of -0.4460 !!! WARNING: ASN 185 has a net charge of -0.6880 !!! WARNING: GLN 189 has a net charge of -0.6880 !!! WARNING: ASN 195 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.889350 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): -34.93700 10.54600 ymin,ymax (A): 0.4030000 41.32000 zmin,zma (A): -0.7420000 54.70300 x,y,z range (A): 45.48300 40.91700 55.44500 scale (grids/A): 2.889350 object centre (A): -12.19550 20.86150 26.98050 number of atom coordinates read : 1944 total number of charged atoms : 1744 net assigned charge : -21.45602 assigned positive charge : 265.3884 centred at (gu) : 91.07417 88.71172 92.67155 assigned negative charge : -286.8443 centred at (gu) : 90.59016 89.26677 92.62872 start vw surface at 0.1300000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 135526 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16695 grid for indexing accessible points = 1.400000 m= 71647 mr = 98450 m= 27267 mr = 59845 m= 6419 mr = 22671 m= 817 mr = 4822 m= 43 mr = 511 m= 0 mr = 21 time to grow re-entrant surface = 0.8099999 no. cavity mid-points inaccessible to solvent = 225 time to turn everything in is 1.440000 number of dielectric boundary points 55399 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 13952 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) : 1.926233 object centre at (A) : -12.19550 20.86150 26.98050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7759183 -1.053613 midg,1,midg; midg,igrid,midg -0.2644671 -0.5100464 1,midg,midg; igrid,midg,midg -0.2238332 -0.3766636 gauss-seidel spectral radius is 0.9992281 estimated iterations to convergence 284 setup time was (sec) 1.760000 now iterating at: 11:02:34 rms-change max change #iterations 8.528605 365.3385 at 10iterations 4.914995 142.7260 at 20iterations 2.801360 61.53484 at 30iterations 1.600550 38.72430 at 40iterations 0.9096330 21.49036 at 50iterations 0.5178991 10.74394 at 60iterations 0.2942294 6.476906 at 70iterations 0.1671713 3.615692 at 80iterations 9.4641820E-02 1.918144 at 90iterations 5.3782959E-02 1.141445 at 100iterations 3.0571051E-02 0.6676226 at 110iterations 1.7325062E-02 0.4010091 at 120iterations 9.8193232E-03 0.1908531 at 130iterations 5.5767423E-03 0.1044426 at 140iterations 3.1699440E-03 6.3604832E-02 at 150iterations 1.8028535E-03 4.1572571E-02 at 160iterations 1.0239255E-03 2.1136761E-02 at 170iterations 5.8485451E-04 1.2262344E-02 at 180iterations finished qdiffx linear iterations at : 11:03:03 total time elapsed so far: 30.60000 # loops : 180 mean,max change (kT/e) : 5.8485451E-04 1.2262344E-02 energy calculations done at 30.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 30.76000 DelPhi exited at 11:03:04 30.764u 0.794s 0:32.30 97.6% 0+0k 0+0io 0pf+0w