[gmx-users] generation of gro file

[Musharaf Ali]

Thank You Justin
But you mean to say that even XYZ coordinates like below format
(18-crown-6) can be directly used in Gromacs.

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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