PFRMAT TS 
TARGET T0061 
AUTHOR 1179-2476-7283 
REMARK 
METHOD  Basic method is AMMP with kohonen neural net 
METHOD  alpha carbons only with 
METHOD  theta ci-1,ci,ci+1 = 90 
METHOD  all atoms have a ~5A vdw exclusion 
METHOD  hydrophobic have a steped attractive potential 
METHOD  based on distances in real structures 
METHOD  hydrophobics = a,c,m,y,f,l,i,v 
METHOD  
METHOD  AMMP script follows 
METHOD echo off; 
METHOD read tar61.ca.fold; 
METHOD use none bond angle step nonbon; 
METHOD setf mxdq 1.; 
METHOD kohonen 200 20 1; 
METHOD cngdel 100; 
METHOD v_maxwell 300; tpac 1000 .00001 300; 
METHOD tpac 10000 .00001 300; 
METHOD cngdel 100; 
METHOD echo off; output tar61.ca.fold; dump atom bond angle step; close;  
METHOD echo; 
METHOD exit; 
METHOD 
METHOD backbone/side chain built with 
METHOD  
METHOD echo off; 
METHOD read tar61.1.ammp; 
METHOD read tar61.1.noel; 
METHOD echo; 
METHOD nzinactive 0 1000000000; 
METHOD use none bond angle hybrid noel; 
METHOD cngdel 100; 
METHOD v_maxwell 300; tpac 10 .00001 300; 
METHOD cngdel 100; 
METHOD use none bond angle hybrid noel; 
METHOD cngdel 100; 
METHOD v_maxwell 300; tpac 10 .00001 300; 
METHOD cngdel 100; 
METHOD use none hybrid; 
METHOD cngdel 10; 
METHOD use none bond angle hybrid noel; 
METHOD cngdel 100; 
METHOD v_maxwell 300; tpac 10 .00001 300; 
METHOD cngdel 100; 
METHOD use none hybrid; 
METHOD cngdel 10; 
METHOD use none bond angle hybrid noel; 
METHOD cngdel 100; 
METHOD v_maxwell 300; tpac 10 .00001 300; 
METHOD cngdel 100; 
METHOD use none hybrid; 
METHOD cngdel 10; 
METHOD use none bond angle hybrid noel; 
METHOD cngdel 100; 
METHOD v_maxwell 300; tpac 10 .00001 300; 
METHOD cngdel 100; 
METHOD  
METHOD  
METHOD use nonbon; 
METHOD setf mxdq 1.; 
METHOD  
METHOD mov ires 1; 
METHOD index iresm numatm; 
METHOD div iresm 100; add iresm 1; 
METHOD loopi end: ires iresm; 
METHOD  
METHOD # search the alpha-beta and beta-gamma angles of ires; 
METHOD # do a lot of checking to make it right; 
METHOD monitor;  #  lets be careful ; 
METHOD  
METHOD serial ic ires c ; 
METHOD jes ic pro.c skip: ; 
METHOD jes ic prx.c skip: ; 
METHOD jes ic css.c skip: ; 
METHOD serial ica ires ca ; 
METHOD serial icb ires cb ; 
METHOD serial icg ires cg ; 
METHOD jl ic 0 skip: ; 
METHOD jl ica 0 skip: ; 
METHOD jl icb 0 skip: ; 
METHOD jg icg 0 next: ; 
METHOD serial icg ires cg1 ; 
METHOD jg icg 0 next: ; 
METHOD serial icg ires og ; 
METHOD jg icg 0 next: ; 
METHOD jl icg 0 skip: ; 
METHOD  
METHOD nop; next: ; 
METHOD  
METHOD tgroup 1 ic ica icb icg 0 6; 
METHOD tsearch 1; 
METHOD  
METHOD serial icd ires cd ; 
METHOD jg icd 0 doit: ; 
METHOD serial icd ires cd1 ; 
METHOD jg icd 0 doit: ; 
METHOD serial icd ires cd2 ; 
METHOD jg icd 0 doit: ; 
METHOD serial icd ires sd; 
METHOD jg icd 0 doit: ; 
METHOD  
METHOD jl icd 0 search: ; 
METHOD nop; doit: ; 
METHOD tgroup 2 ica icb icg icd  0 6; 
METHOD tsearch 1 2; 
METHOD jes ic tyr.c search: ; 
METHOD jes ic phe.c search: ; 
METHOD jes ic his.c search: ; 
METHOD serial ice ires ce; 
METHOD jg ice 0 doit2: ; 
METHOD serial ice ires ce1; 
METHOD jg ice 0 doit2: ; 
METHOD serial ice ires ce2; 
METHOD jg ice 0 doit2: ; 
METHOD serial ice ires ne; 
METHOD jg ice 0 doit2: ; 
METHOD jl ice 0 search: ; 
METHOD nop; doit2: ; 
METHOD tgroup 3 icb icg icd ice 0 6; 
METHOD tsearch 1 2 3; 
METHOD search: ; 
METHOD  
METHOD monitor; 
METHOD skip: ; #default exit; 
METHOD end: ; 
METHOD cngdel 100; 
METHOD active 0 10000000; 
METHOD cngdel 100; 
METHOD use none bond angle hybrid torsion nonbon; 
METHOD cngdel 100; 
METHOD echo off; output tar61.1.built.ammp; dump atom bond angle hybrid torsion; 
METHOD close;  
METHOD output tar611b.pdb; dump pdb; close;  
METHOD echo; 
METHOD exit; 
METHOD  
METHOD this was followed by cng gradeients and molecular dynamics 
METHOD  TRP 82,16 required manual work in the 2,4 models 
METHOD   
METHOD models 1,2 are enantiomorphs as this method is achiral 
METHOD models 3,4 are the raw traces of models 1,2 
METHOD Therefore only one of 1,2  is "correct" 
METHOD models 1,3 are the 'left handed solution' because it built easier 
METHOD 
MODEL 4 
PARENT N/A 
ATOM      1  CA  ALA     1     -14.390 101.528-127.836  1.00 10.00 
ATOM      2  CA  ASP     2     -14.167  99.880-131.321  1.00 10.00 
ATOM      3  CA  ALA     3     -10.843  98.885-129.860  1.00 10.00 
ATOM      4  CA  GLN     4      -9.178  99.745-133.177  1.00 10.00 
ATOM      5  CA  LYS     5      -8.930 103.413-131.933  1.00 10.00 
ATOM      6  CA  ALA     6      -7.556 102.158-128.577  1.00 10.00 
ATOM      7  CA  ALA     7      -9.492 104.722-126.560  1.00 10.00 
ATOM      8  CA  ASP     8      -9.100 107.472-129.236  1.00 10.00 
ATOM      9  CA  ASN     9      -5.353 106.677-129.659  1.00 10.00 
ATOM     10  CA  LYS    10      -4.423 110.144-128.319  1.00 10.00 
ATOM     11  CA  LYS    11      -6.404 109.388-125.096  1.00 10.00 
ATOM     12  CA  PRO    12      -3.391 107.455-123.699  1.00 10.00 
ATOM     13  CA  VAL    13      -4.679 104.267-125.317  1.00 10.00 
ATOM     14  CA  ASN    14      -1.043 102.890-125.241  1.00 10.00 
ATOM     15  CA  SER    15      -1.615 101.299-128.691  1.00 10.00 
ATOM     16  CA  TRP    16      -4.235  98.933-127.184  1.00 10.00 
ATOM     17  CA  THR    17      -1.591  97.546-124.752  1.00 10.00 
ATOM     18  CA  CYS    18      -4.332  95.828-122.667  1.00 10.00 
ATOM     19  CA  GLU    19      -1.813  95.376-119.824  1.00 10.00 
ATOM     20  CA  ASP    20      -4.816  94.819-117.488  1.00 10.00 
ATOM     21  CA  PHE    21      -6.689  98.011-118.552  1.00 10.00 
ATOM     22  CA  LEU    22      -8.985  96.058-120.931  1.00 10.00 
ATOM     23  CA  ALA    23     -11.937  98.206-119.740  1.00 10.00 
ATOM     24  CA  VAL    24     -13.573  95.459-117.670  1.00 10.00 
ATOM     25  CA  ASP    25     -14.707  97.860-114.930  1.00 10.00 
ATOM     26  CA  GLU    26     -18.316  96.568-115.540  1.00 10.00 
ATOM     27  CA  SER    27     -19.501 100.086-116.725  1.00 10.00 
ATOM     28  CA  PHE    28     -16.106 100.863-118.447  1.00 10.00 
ATOM     29  CA  GLN    29     -16.341 104.358-116.898  1.00 10.00 
ATOM     30  CA  PRO    30     -15.289 102.924-113.503  1.00 10.00 
ATOM     31  CA  THR    31     -11.686 104.221-114.136  1.00 10.00 
ATOM     32  CA  ALA    32     -11.479 102.295-117.441  1.00 10.00 
ATOM     33  CA  VAL    33      -7.681 102.496-117.368  1.00 10.00 
ATOM     34  CA  GLY    34      -8.014 106.228-118.062  1.00 10.00 
ATOM     35  CA  PHE    35      -7.794 105.379-121.812  1.00 10.00 
ATOM     36  CA  ALA    36     -10.790 107.523-122.688  1.00 10.00 
ATOM     37  CA  GLU    37     -12.792 106.235-119.702  1.00 10.00 
ATOM     38  CA  ALA    38     -13.034 102.905-121.623  1.00 10.00 
ATOM     39  CA  LEU    39     -14.085 105.061-124.570  1.00 10.00 
ATOM     40  CA  ASN    40     -17.269 106.518-122.748  1.00 10.00 
ATOM     41  CA  ASN    41     -19.586 105.552-125.595  1.00 10.00 
ATOM     42  CA  LYS    42     -21.941 103.906-123.047  1.00 10.00 
ATOM     43  CA  ASP    43     -24.239 102.826-125.969  1.00 10.00 
ATOM     44  CA  LYS    44     -24.506  99.291-124.446  1.00 10.00 
ATOM     45  CA  PRO    45     -23.815  97.792-127.917  1.00 10.00 
ATOM     46  CA  GLU    46     -20.325  99.330-127.854  1.00 10.00 
ATOM     47  CA  ASP    47     -19.045  96.303-125.742  1.00 10.00 
ATOM     48  CA  ALA    48     -15.504  96.969-126.999  1.00 10.00 
ATOM     49  CA  VAL    49     -14.552  98.537-123.626  1.00 10.00 
ATOM     50  CA  LEU    50     -17.330 101.136-123.894  1.00 10.00 
ATOM     51  CA  ASP    51     -19.870  99.162-121.753  1.00 10.00 
ATOM     52  CA  VAL    52     -17.257  96.632-120.537  1.00 10.00 
ATOM     53  CA  GLN    53     -20.045  94.009-120.425  1.00 10.00 
ATOM     54  CA  GLY    54     -17.510  91.203-121.179  1.00 10.00 
ATOM     55  CA  ILE    55     -15.491  93.594-123.355  1.00 10.00 
ATOM     56  CA  ALA    56     -12.474  92.593-121.240  1.00 10.00 
ATOM     57  CA  THR    57     -12.189  89.319-123.220  1.00 10.00 
ATOM     58  CA  VAL    58      -9.502  91.027-125.406  1.00 10.00 
ATOM     59  CA  THR    59     -11.074  89.254-128.406  1.00 10.00 
ATOM     60  CA  PRO    60     -14.118  91.605-127.993  1.00 10.00 
ATOM     61  CA  ALA    61     -11.717  94.527-128.579  1.00 10.00 
ATOM     62  CA  ILE    62     -11.436  95.452-124.899  1.00 10.00 
ATOM     63  CA  VAL    63      -8.269  97.499-125.514  1.00 10.00 
ATOM     64  CA  GLN    64     -10.520 100.429-125.077  1.00 10.00 
ATOM     65  CA  ALA    65      -9.047 101.056-121.601  1.00 10.00 
ATOM     66  CA  CYS    66      -5.502 100.466-122.773  1.00 10.00 
ATOM     67  CA  THR    67      -3.811 102.994-120.377  1.00 10.00 
ATOM     68  CA  GLN    68      -2.003 100.220-118.327  1.00 10.00 
ATOM     69  CA  ASP    69      -3.200 101.833-115.091  1.00 10.00 
ATOM     70  CA  LYS    70      -4.598  98.437-113.866  1.00 10.00 
ATOM     71  CA  GLN    71      -7.841 100.125-112.673  1.00 10.00 
ATOM     72  CA  ALA    72      -9.700  98.185-115.405  1.00 10.00 
ATOM     73  CA  ASN    73      -8.834  94.796-113.796  1.00 10.00 
ATOM     74  CA  PHE    74      -9.279  93.201-117.257  1.00 10.00 
ATOM     75  CA  LYS    75     -10.044  89.816-115.539  1.00 10.00 
ATOM     76  CA  ASP    76      -6.768  88.597-116.913  1.00 10.00 
ATOM     77  CA  LYS    77      -8.225  88.445-120.504  1.00 10.00 
ATOM     78  CA  VAL    78      -6.715  91.912-121.305  1.00 10.00 
ATOM     79  CA  LYS    79      -3.326  90.525-120.189  1.00 10.00 
ATOM     80  CA  GLY    80      -1.605  91.418-123.526  1.00 10.00 
ATOM     81  CA  GLU    81      -4.514  89.947-125.458  1.00 10.00 
ATOM     82  CA  TRP    82      -5.580  93.536-126.415  1.00 10.00 
ATOM     83  CA  ASP    83      -2.195  93.882-128.255  1.00 10.00 
ATOM     84  CA  LYS    84      -3.514  95.846-131.319  1.00 10.00 
ATOM     85  CA  ILE    85      -7.090  95.991-129.840  1.00 10.00 
ATOM     86  CA  LYS    86      -7.716  92.417-131.102  1.00 10.00 
ATOM     87  CA  LYS    87     -10.182  93.734-133.745  1.00 10.00 
ATOM     88  CA  ASP    88      -7.229  95.396-135.580  1.00 10.00 
TER 
END    
