[gmx-users] generation of gro file

Sun Aug 18 17:25:37 CEST 2013

Dear Justin
Thanks a lot.
will definitely do it.

warm regards

On Sun, Aug 18, 2013 at 10:53 AM, Musharaf Ali <skmali786 at gmail.com> wrote:

> Dear Justin
> Again thanks. Actually the problem arises in the running of pdb2gmx of pdb
> file of crown ether. I have generated the pdb file from xyz coordinates
> using openbabel. The pdb file looks like below.
>
>
> COMPND D:\data-structure\18c6.xyz
>
> AUTHOR GENERATED BY OPEN BABEL 2.3.2
>
> HETATM 1 O LIG 1 0.000 0.000 0.000 1.00 0.00 O
>
> HETATM 2 C LIG 1 0.000 0.000 1.400 1.00 0.00 C
>
> HETATM 3 C LIG 1 1.367 0.000 1.883 1.00 0.00 C
>
> HETATM 4 H LIG 1 -0.513 0.889 1.763 1.00 0.00 H
>
> HETATM 5 H LIG 1 -0.513 -0.889 1.763 1.00 0.00 H
>
> HETATM 6 H LIG 1 1.367 0.000 2.972 1.00 0.00 H
>
> HETATM 7 O LIG 1 2.027 -1.143 1.417 1.00 0.00 O
>
> HETATM 8 H LIG 1 1.880 0.889 1.520 1.00 0.00 H
>
> HETATM 9 C LIG 1 3.347 -1.143 1.883 1.00 0.00 C
>
> HETATM 10 C LIG 1 4.031 -2.327 1.400 1.00 0.00 C
>
> HETATM 11 H LIG 1 3.860 -0.254 1.520 1.00 0.00 H
>
> HETATM 12 H LIG 1 3.347 -1.143 2.972 1.00 0.00 H
>
> HETATM 13 H LIG 1 5.057 -2.327 1.763 1.00 0.00 H
>
> HETATM 14 H LIG 1 3.517 -3.216 1.763 1.00 0.00 H
>
> HETATM 15 O LIG 1 4.031 -2.327 -0.000 1.00 0.00 O
>
> HETATM 16 C LIG 1 4.690 -3.470 -0.467 1.00 0.00 C
>
> HETATM 17 C LIG 1 4.690 -3.470 -1.917 1.00 0.00 C
>
> HETATM 18 H LIG 1 5.717 -3.470 -0.104 1.00 0.00 H
>
> HETATM 19 H LIG 1 4.177 -4.359 -0.104 1.00 0.00 H
>
> HETATM 20 H LIG 1 5.204 -4.359 -2.280 1.00 0.00 H
>
> HETATM 21 O LIG 1 3.371 -3.470 -2.383 1.00 0.00 O
>
> HETATM 22 H LIG 1 5.204 -2.581 -2.280 1.00 0.00 H
>
> HETATM 23 C LIG 1 3.371 -3.470 -3.783 1.00 0.00 C
>
> HETATM 24 C LIG 1 2.003 -3.470 -4.267 1.00 0.00 C
>
> HETATM 25 H LIG 1 3.884 -2.581 -4.146 1.00 0.00 H
>
> HETATM 26 H LIG 1 3.884 -4.359 -4.146 1.00 0.00 H
>
> HETATM 27 H LIG 1 2.003 -3.470 -5.356 1.00 0.00 H
>
> HETATM 28 H LIG 1 1.490 -4.359 -3.904 1.00 0.00 H
>
> HETATM 29 O LIG 1 1.343 -2.327 -3.800 1.00 0.00 O
>
> HETATM 30 C LIG 1 0.024 -2.327 -4.267 1.00 0.00 C
>
> HETATM 31 C LIG 1 -0.660 -1.143 -3.783 1.00 0.00 C
>
> HETATM 32 H LIG 1 0.024 -2.327 -5.356 1.00 0.00 H
>
> HETATM 33 H LIG 1 -0.490 -3.216 -3.904 1.00 0.00 H
>
> HETATM 34 H LIG 1 -1.687 -1.143 -4.146 1.00 0.00 H
>
> HETATM 35 O LIG 1 -0.660 -1.143 -2.383 1.00 0.00 O
>
> HETATM 36 H LIG 1 -0.147 -0.254 -4.146 1.00 0.00 H
>
> HETATM 37 C LIG 1 -1.320 0.000 -1.917 1.00 0.00 C
>
> HETATM 38 C LIG 1 -1.320 0.000 -0.467 1.00 0.00 C
>
> HETATM 39 H LIG 1 -0.807 0.889 -2.280 1.00 0.00 H
>
> HETATM 40 H LIG 1 -2.347 0.000 -2.280 1.00 0.00 H
>
> HETATM 41 H LIG 1 -1.833 0.889 -0.104 1.00 0.00 H
>
> HETATM 42 H LIG 1 -1.833 -0.889 -0.104 1.00 0.00 H
>
> CONECT 1 38 2
>
> CONECT 2 1 5 4 3
>
> CONECT 2
>
> CONECT 3 2 7 8 6
>
> CONECT 3
>
> CONECT 4 2
>
> CONECT 5 2
>
> CONECT 6 3
>
> CONECT 7 9 3
>
> CONECT 8 3
>
> CONECT 9 10 7 11 12
>
> CONECT 9
>
> CONECT 10 15 13 14 9
>
> CONECT 10
>
> CONECT 11 9
>
> CONECT 12 9
>
> CONECT 13 10
>
> CONECT 14 10
>
> CONECT 15 16 10
>
> CONECT 16 17 18 19 15
>
> CONECT 16
>
> CONECT 17 21 22 20 16
>
> CONECT 17
>
> CONECT 18 16
>
> CONECT 19 16
>
> CONECT 20 17
>
> CONECT 21 23 17
>
> CONECT 22 17
>
> CONECT 23 24 26 25 21
>
> CONECT 23
>
> CONECT 24 27 28 29 23
>
> CONECT 24
>
> CONECT 25 23
>
> CONECT 26 23
>
> CONECT 27 24
>
> CONECT 28 24
>
> CONECT 29 24 30
>
> CONECT 30 32 33 29 31
>
> CONECT 30
>
> CONECT 31 30 36 34 35
>
> CONECT 31
>
> CONECT 32 30
>
> CONECT 33 30
>
> CONECT 34 31
>
> CONECT 35 31 37
>
> CONECT 36 31
>
> CONECT 37 35 39 40 38
>
> CONECT 37
>
> CONECT 38 37 41 42 1
>
> CONECT 38
>
> CONECT 39 37
>
> CONECT 40 37
>
> CONECT 41 38
>
> CONECT 42 38
>
> MASTER 0 0 0 0 0 0 0 0 42 0 42 0
>
> END
>
> Now my query is whether this pdb format i can directly used for pdb2gmx or
> i have to change the "LIG" temr to OPLS force field term. If you can guide
> here then the problem will be sorted out.
>
>
>
> warm regards
>
> SMA
>
>
> On Sat, Aug 17, 2013 at 8:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> 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>
>>>> <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 <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 <jalemkul at outerbanks.umaryland.edu>| (410) 706-7441
>>
>> ==============================**====================
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>
>