[gmx-users] A very strange problem about version of pdb2gmx

[英雄不再寂寞]

Dear gmxers,
  Yesterday, I posted a mail titled "pdb2gmx stop at "AtomType 1" " where I mentioned that I used gmx-4.5.1. The resulting problem is again posted below. Today, I turn to the gmx-4.0.7, and use the same pdb and rtp files with the name modified to compatible to the version. Strangely, it is found that the pdb2gmx of this version can generate the top file without any errors. Could you give me clues to why the latest version can not whereas the older version can? To get the clear help, my pdb and rtp files are also posted below. Thanks a lot for any reply.
 Chaofu Wu, Dr.
  
 My command line and the screen output:
xiaowu759 at linux-s38y:~/workshop> pdb2gmx -f deta.pdb -o deta.gro -p deta.top -i deta.itp -ter
                         :-)  G  R  O  M  A  C  S  (-:
               Gromacs Runs One Microsecond At Cannonball Speeds
                            :-)  VERSION 4.5.1  (-:
......
Opening force field file oplsaa.ff/aminoacids.r2b
Reading deta.pdb...
Read 20 atoms
Analyzing pdb file
Splitting PDB chains based on TER records or changing chain id.
There are 1 chains and 0 blocks of water and 1 residues with 20 atoms
  chain  #res #atoms
  1 ' '     1     20  
All occupancies are one
Opening force field file oplsaa.ff/atomtypes.atp
Atomtype 1
 
My pdb file:
ATOM      1  N1  MOL     1      -5.199   1.343   0.334  1.00  0.00           N    
ATOM      2  C2  MOL     1      -4.582   0.639   1.470  1.00  0.00           C    
ATOM      3  C3  MOL     1      -3.897   1.462   2.593  1.00  0.00           C    
ATOM      4  N4  MOL     1      -3.194   0.615   3.574  1.00  0.00           N    
ATOM      5  C5  MOL     1      -2.373   1.331   4.566  1.00  0.00           C    
ATOM      6  C6  MOL     1      -1.520   0.397   5.464  1.00  0.00           C    
ATOM      7  N7  MOL     1      -0.684   1.133   6.432  1.00  0.00           N    
ATOM      8  H12 MOL     1      -4.614   2.067  -0.035  1.00  0.00           H    
ATOM      9  H11 MOL     1      -6.128   1.694   0.483  1.00  0.00           H    
ATOM     10  H22 MOL     1      -3.826  -0.053   1.056  1.00  0.00           H    
ATOM     11  H21 MOL     1      -5.345  -0.016   1.926  1.00  0.00           H    
ATOM     12  H31 MOL     1      -4.628   2.144   3.065  1.00  0.00           H    
ATOM     13  H32 MOL     1      -3.141   2.116   2.124  1.00  0.00           H    
ATOM     14  H41 MOL     1      -3.854   0.018   4.043  1.00  0.00           H    
ATOM     15  H51 MOL     1      -2.980   2.003   5.204  1.00  0.00           H    
ATOM     16  H52 MOL     1      -1.679   1.992   4.016  1.00  0.00           H    
ATOM     17  H62 MOL     1      -0.857  -0.180   4.795  1.00  0.00           H    
ATOM     18  H61 MOL     1      -2.188  -0.346   5.939  1.00  0.00           H    
ATOM     19  H72 MOL     1      -0.023   0.541   6.916  1.00  0.00           H    
ATOM     20  H71 MOL     1      -1.253   1.554   7.143  1.00  0.00           H    
TER
 My rtp file:
[ DET ]
 [ atoms ]
    N1    opls_900    -0.900      1
   H11    opls_909     0.360      1
   H12    opls_909     0.360      1
    C2    opls_906     0.060      1
   H21    opls_911     0.060      1
   H22    opls_911     0.060      1
    C3    opls_907     0.080      2
   H31    opls_911     0.060      2
   H32    opls_911     0.060      2
    N4    opls_901    -0.780      2
   H41    opls_910     0.380      2
    C5    opls_907     0.080      2
   H51    opls_911     0.060      2
   H52    opls_911     0.060      2
    C6    opls_906     0.060      3
   H61    opls_911     0.060      3
   H62    opls_911     0.060      3
    N7    opls_900    -0.900      3
   H71    opls_909     0.360      3
   H72    opls_909     0.360      3
 [ bonds ]
    N1   H11
    N1   H12
    N1    C2
    C2   H21
    C2   H22
    C2    C3
    C3   H31
    C3   H32
    C3    N4
    N4   H41
    N4    C5
    C5   H51
    C5   H52
    C5    C6
    C6   H61
    C6   H62
    C6    N7
    N7   H71
    N7   H72
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