[gmx-users] the pdb file => input / output error

[Justin A. Lemkul]

Quoting Chih-Ying Lin <chihying2008 at gmail.com>:

> HI
> Here is my pdb file.
> When I typed
> pdb2gmx -f xx.pdb -p xx.top -o xx.gro
>
> it showed input / output error.

It is better to provide the exact error message.

> Could anyone point out what the mistakes I made?

I can see one.  You're using pdb2gmx to process some random molecule called
'MOL.'  You'll likely get this error:

http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database

The information at that page will serve you well.

-Justin

> Thanks a lot
> Lin
>
>
> REMARK  MOL
> ATOM      1  C3  MOL     1       3.747   1.679   1.116
> ATOM      2  H3  MOL     1       4.400   1.022   1.684
> ATOM      3  C2  MOL     1       2.378   1.705   1.382
> ATOM      4  H2  MOL     1       1.963   1.062   2.156
> ATOM      5  C1  MOL     1       1.544   2.555   0.658
> ATOM      6  H1  MOL     1       0.477   2.581   0.870
> ATOM      7  C6  MOL     1       2.077   3.378  -0.333
> ATOM      8  H5  MOL     1       1.430   4.052  -0.892
> ATOM      9  C5  MOL     1       3.444   3.339  -0.608
> ATOM     10  H4  MOL     1       3.865   3.979  -1.378
> ATOM     11  C4  MOL     1       4.281   2.486   0.110
> ATOM     12  N1  MOL     1       5.694   2.490  -0.176
> ATOM     13  N2  MOL     1       6.272   1.500  -0.716
> ATOM     14  C7  MOL     1       5.574   0.272  -1.007
> ATOM     15  C8  MOL     1       5.900  -0.877  -0.286
> ATOM     16  H6  MOL     1       6.660  -0.825   0.489
> ATOM     17  C9  MOL     1       5.261  -2.085  -0.563
> ATOM     18  H7  MOL     1       5.524  -2.980  -0.003
> ATOM     19  C10 MOL     1       4.289  -2.144  -1.561
> ATOM     20  H8  MOL     1       3.786  -3.084  -1.776
> ATOM     21  C11 MOL     1       3.964  -0.998  -2.286
> ATOM     22  H9  MOL     1       3.205  -1.042  -3.065
> ATOM     23  C12 MOL     1       4.615   0.205  -2.018
> ATOM     24  H10 MOL     1       4.368   1.098  -2.587
> TER
> END
>



========================================

Justin A. Lemkul
Graduate Research Assistant
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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