Wed Dec 28 11:01:53 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 11:01:54 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 !!! 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: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 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: 0.5703391 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): -34.86100 9.945001 ymin,ymax (A): 0.7150000 40.87400 zmin,zma (A): -2.459000 59.96000 x,y,z range (A): 44.80600 40.15900 62.41900 scale (grids/A): 0.5703391 object centre (A): -12.45800 20.79450 28.75050 number of atom coordinates read : 1958 total number of charged atoms : 1758 net assigned charge : -21.95202 assigned positive charge : 266.4024 centred at (gu) : 90.43719 89.70974 89.48816 assigned negative charge : -288.3542 centred at (gu) : 90.34061 89.83965 89.52200 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 4253 nv = 96 ne = 84 npr = 40154 no. pairs analyzed = 40154 no. exposed pairs = 2445 no. arc points = 17098 no. surface atoms = 836 nbur = 1122 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 175 mr = 2265 m= 0 mr = 11 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1645 ## 148 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 5213 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.4539689E-09 -3.3491785E-09 midg,1,midg; midg,igrid,midg -2.2397655E-09 -4.4670236E-09 1,midg,midg; igrid,midg,midg -3.9988297E-09 -2.6866998E-09 gauss-seidel spectral radius is 0.9840524 estimated iterations to convergence 65 setup time was (sec) 0.5100000 now iterating at: 11:01:54 rms-change max change #iterations 7.7847250E-02 15.07211 at 10iterations 5.7207714E-03 1.057734 at 20iterations 4.3928446E-04 7.0770264E-02 at 30iterations 3.2529402E-05 6.1645508E-03 at 40iterations 2.4675508E-06 4.7302246E-04 at 50iterations finished qdiffx linear iterations at : 11:01:59 total time elapsed so far: 4.620000 # loops : 50 mean,max change (kT/e) : 2.4675508E-06 4.7302246E-04 energy calculations done at 4.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.780000 DelPhi exited at 11:01:59 4.788u 0.400s 0:05.58 92.8% 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 Wed Dec 28 2011 at 11:01:59 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 !!! 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: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 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: 1.711017 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): -34.86100 9.945001 ymin,ymax (A): 0.7150000 40.87400 zmin,zma (A): -2.459000 59.96000 x,y,z range (A): 44.80600 40.15900 62.41900 scale (grids/A): 1.711017 object centre (A): -12.45800 20.79450 28.75050 number of atom coordinates read : 1958 total number of charged atoms : 1758 net assigned charge : -21.95202 assigned positive charge : 266.4024 centred at (gu) : 91.31169 89.12936 88.46436 assigned negative charge : -288.3542 centred at (gu) : 91.02190 89.51933 88.56606 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 46127 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17098 grid for indexing accessible points = 1.400000 m= 15201 mr = 31354 m= 1658 mr = 11005 m= 51 mr = 829 m= 2 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 19849 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 13666 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) : 0.5703391 object centre at (A) : -12.45800 20.79450 28.75050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9096901E-02 -2.9462256E-02 midg,1,midg; midg,igrid,midg -1.1369663E-02 -2.2913760E-02 1,midg,midg; igrid,midg,midg -1.2980880E-02 -1.6341519E-02 gauss-seidel spectral radius is 0.9982274 estimated iterations to convergence 189 setup time was (sec) 0.7200000 now iterating at: 11:02:00 rms-change max change #iterations 2.913758 160.9484 at 10iterations 1.217770 52.11047 at 20iterations 0.5125149 24.14129 at 30iterations 0.2160389 9.075302 at 40iterations 9.1287211E-02 3.899963 at 50iterations 3.8304202E-02 1.658617 at 60iterations 1.6139427E-02 0.6355457 at 70iterations 6.7723342E-03 0.2819932 at 80iterations 2.8551833E-03 0.1195321 at 90iterations 1.2041214E-03 4.9345016E-02 at 100iterations 5.0645357E-04 1.9760609E-02 at 110iterations 2.1338799E-04 9.5300674E-03 at 120iterations finished qdiffx linear iterations at : 11:02:10 total time elapsed so far: 10.48000 # loops : 120 mean,max change (kT/e) : 2.1338799E-04 9.5300674E-03 energy calculations done at 10.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.66000 DelPhi exited at 11:02:11 10.663u 0.434s 0:11.89 93.2% 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 Wed Dec 28 2011 at 11:02:11 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 !!! 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: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 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: 2.566526 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): -34.86100 9.945001 ymin,ymax (A): 0.7150000 40.87400 zmin,zma (A): -2.459000 59.96000 x,y,z range (A): 44.80600 40.15900 62.41900 scale (grids/A): 2.566526 object centre (A): -12.45800 20.79450 28.75050 number of atom coordinates read : 1958 total number of charged atoms : 1758 net assigned charge : -21.95202 assigned positive charge : 266.4024 centred at (gu) : 91.96754 88.69408 87.69671 assigned negative charge : -288.3542 centred at (gu) : 91.53280 89.27893 87.84914 start vw surface at 0.1100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 106613 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17098 grid for indexing accessible points = 1.400000 m= 51428 mr = 76016 m= 15831 mr = 41660 m= 2599 mr = 12411 m= 231 mr = 1659 m= 5 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9900000 number of dielectric boundary points 44840 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 14054 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) : 1.711017 object centre at (A) : -12.45800 20.79450 28.75050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5072348 -0.4639313 midg,1,midg; midg,igrid,midg -0.1388142 -0.3093624 1,midg,midg; igrid,midg,midg -0.1660890 -0.2274109 gauss-seidel spectral radius is 0.9991155 estimated iterations to convergence 266 setup time was (sec) 1.330000 now iterating at: 11:02:13 rms-change max change #iterations 7.212109 268.8176 at 10iterations 4.000008 110.7457 at 20iterations 2.206765 63.31673 at 30iterations 1.212475 31.08532 at 40iterations 0.6629428 18.76237 at 50iterations 0.3637023 8.752120 at 60iterations 0.1987867 5.050758 at 70iterations 0.1085927 2.812008 at 80iterations 5.9314482E-02 1.348845 at 90iterations 3.2229956E-02 0.7319956 at 100iterations 1.7605485E-02 0.5054417 at 110iterations 9.5747923E-03 0.2309103 at 120iterations 5.2287588E-03 0.1171846 at 130iterations 2.8465576E-03 6.6884995E-02 at 140iterations 1.5462114E-03 3.6716938E-02 at 150iterations 8.4395218E-04 2.0557404E-02 at 160iterations 4.5877881E-04 1.1608362E-02 at 170iterations 2.4972585E-04 6.2561035E-03 at 180iterations finished qdiffx linear iterations at : 11:02:28 total time elapsed so far: 16.54000 # loops : 180 mean,max change (kT/e) : 2.4972585E-04 6.2561035E-03 energy calculations done at 16.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.70000 DelPhi exited at 11:02:30 16.706u 0.474s 0:18.67 91.9% 0+0k 0+0io 0pf+0w