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 3 
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    
