[gmx-users] generation of gro file

[Justin Lemkul]

On 8/17/13 10:58 AM, Musharaf Ali wrote:
> Thank You Justin
> But you mean to say that even XYZ coordinates like below format
> (18-crown-6) can be directly used in Gromacs.
>

I don't know.  I seem to recall some discussion about .xyz files some time ago, 
but I forget the outcome.  My point was that most new users think that .gro 
files are absolutely required, which is not true.  Numerous file formats are 
accepted.  Check the manual and Gromacs website.  You may need to convert to 
another format, but it doesn't necessarily have to be .gro.

-Justin

> O 0.000000 0.000000 0.000000
>
> C 0.000000 0.000000 1.400000
>
> C 1.367075 0.000000 1.883328
>
> H -0.513360 0.889165 1.763000
>
> H -0.513360 -0.889165 1.763000
>
> H 1.367079 0.000000 2.972328
>
> O 2.027040 -1.143095 1.416659
>
> H 1.880433 0.889165 1.520326
>
> C 3.346974 -1.143095 1.883320
>
> C 4.030509 -2.327015 1.399984
>
> H 3.860332 -0.253930 1.520318
>
> H 3.346978 -1.143095 2.972320
>
> H 5.057229 -2.327015 1.762981
>
> H 3.517151 -3.216180 1.762986
>
> O 4.030503 -2.327015 -0.000016
>
> C 4.690468 -3.470110 -0.466685
>
> C 4.690462 -3.470110 -1.916685
>
> H 5.717188 -3.470110 -0.103689
>
> H 4.177110 -4.359275 -0.103683
>
> H 5.203820 -4.359275 -2.279687
>
> O 3.370528 -3.470110 -2.383346
>
> H 5.203820 -2.580946 -2.279687
>
> C 3.370522 -3.470110 -3.783346
>
> C 2.003447 -3.470110 -4.266674
>
> H 3.883880 -2.580946 -4.146348
>
> H 3.883880 -4.359275 -4.146348
>
> H 2.003443 -3.470110 -5.355674
>
> H 1.490089 -4.359275 -3.903672
>
> O 1.343483 -2.327015 -3.800005
>
> C 0.023548 -2.327015 -4.266667
>
> C -0.659986 -1.143095 -3.783331
>
> H 0.023544 -2.327015 -5.355667
>
> H -0.489810 -3.216180 -3.903665
>
> H -1.686707 -1.143095 -4.146327
>
> O -0.659981 -1.143095 -2.383331
>
> H -0.146628 -0.253930 -4.146333
>
> C -1.319945 0.000000 -1.916662
>
> C -1.319940 0.000000 -0.466662
>
> H -0.806587 0.889165 -2.279664
>
> H -2.346666 0.000000 -2.279658
>
> H -1.833298 0.889165 -0.103660
>
> H -1.833298 -0.889165 -0.103660
>
>
> On Sat, Aug 17, 2013 at 3:53 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 8/16/13 10:50 PM, Musharaf Ali wrote:
>>
>>> Hi
>>> could somebody help how to generate grow file from xyz coordinates
>>> specially for crown ether type molecules.
>>>
>>
>> The specifications of the .gro format are described here:
>>
>> http://manual.gromacs.org/**online/gro.html<http://manual.gromacs.org/online/gro.html>
>>
>> Note that there is no requirement to use .gro files in Gromacs.  Most
>> formats will be recognized.
>>
>>
>>   Here the xyz coordinates are attached for 18-crown-6. Thank in advance.
>>>
>>
>> FYI the mailing list does not accept attachments.
>>
>> -Justin
>>
>> --
>> ==============================**====================
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> |
>> (410) 706-7441
>>
>> ==============================**====================
>> --
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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