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

[Tsjerk Wassenaar]

Hi,

Justin is correct, but that wouldn't explain the input/output error.
That will happen either when the input is not found (xx.pdb; carefully
check for typo's) or when you're not allowed to read/write, because of
a full disk or permissions. Check whether you have read permission on
the input file, and write permission in the directory.

If that's not the problem, post the output from pdb2gmx (as Justin
pointed out is always the smartest thing to do when posting to a
list... see http://catb.org/~esr/faqs/smart-questions.html).

Cheers,

Tsjerk

On Wed, May 28, 2008 at 12:50 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623