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

[Justin A. Lemkul]

英雄不再寂寞 wrote:
> 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.

Your system works for me under version 4.5.1, after fixing the naming mismatch 
you have between your .pdb file ("MOL") and .rtp file ("DET").  I suppose your 
actual input files have the correct names, though, otherwise this combination 
would have generated a fatal error, not a hang.

-Justin

> Chaofu Wu, Dr.
>  
> My command line and the screen output:
> xiaowu759 at linux-s38y:~/workshop 
> <mailto: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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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