[gmx-users] generation of gro file

Musharaf Ali skmali786 at gmail.com
Sun Aug 18 07:23:28 CEST 2013


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
>
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>
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