[gmx-users] .gro file problem

[Justin Lemkul]

On 10/29/12 9:59 AM, Albert wrote:
> On 10/28/2012 09:06 PM, Justin Lemkul wrote:
>> Visual inspection with a text editor should tell you what's wrong. Either the
>> file is incomplete (i.e. header or box vectors missing) or the coordinates are
>> large (indicating the system became unstable at some point).  The fact that
>> VMD loads the file suggests that the latter may be true.  An incomplete file
>> would not load, but one with screwy coordinates still would.
>>
>> -Justin
>>
>> --
>
> Hello Justin:
>
>   thanks a lot for kind advices.
>
>   I check the file with gedit and I didn't find anything unusual within the text
> comparing with the original .gro file. They have the exact the same row and
> columns.
>
>
> Generated by trjconv : MOR t= 116.00
> Generated by trjconv : MOR t= 1160000.00000

You shouldn't have two separate title lines.  I don't know how trjconv would 
have produced garbled output like this, but I suspect it's the cause of your 
problems.

-Justin

> 48328
>     65MET      N    1   4.934   1.182   7.535  0.0471  0.2110  0.3278
>     65MET    HT1    2   4.975   1.148   7.620 -2.1539 -2.5438  0.4303
>     65MET    HT2    3   4.879   1.108   7.497  0.2031  0.2641 -0.0060
>     65MET     CA    4   5.035   1.229   7.441 -0.1568 -0.5819 -0.2954
>     65MET     HA    5   5.090   1.312   7.481  2.2845 -1.6076 -1.3193
>     65MET     CB    6   5.149   1.126   7.437  0.4809  0.1027  0.0700
>     65MET    HB1    7   5.166   1.099   7.544 -2.2162  1.7701  1.0201
>     65MET    HB2    8   5.117   1.032   7.386 -3.2381  0.4514  1.4551
>     65MET     CG    9   5.283   1.173   7.379  0.1733  0.3849 -0.4145
>     65MET    HG1   10   5.340   1.078   7.384  0.4424  0.6052  2.0263
> .
> .
> .
>   9511CL      CL48320   2.101   1.980   2.259  0.0337 -0.1667  0.2316
>   9512CL      CL48321   4.165   3.237  10.196 -0.4009  0.1697  0.4481
>   9513CL      CL48322   5.414   4.564   9.686 -0.1624 -0.0698 -0.2503
>   9514CL      CL48323   2.032   1.126   1.460  0.0876 -0.4133 -0.1336
>   9515CL      CL48324   3.278   3.994   9.006  0.1073 -0.1139  0.6701
>   9516CL      CL48325   1.793   3.569   9.888  0.0911  0.2208 -0.0272
>   9517CL      CL48326   1.046   2.735   1.322  0.1044  0.2204  0.4059
>   9518CL      CL48327   3.384   4.016   1.983  0.0078  0.1266 -0.1903
>   9519CL      CL48328   0.044   3.730   0.932 -0.2059  0.0577  0.3350
>     6.69862   6.69862  10.42296
>
> thank you very much

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
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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