[gmx-users] editconf- pdb to gro format

[Justin Lemkul]

On 4/1/13 8:55 PM, Juliette N. wrote:
> Hi Justin
>
> I tried several residue names, 1Ethylene, 1Eth  but editconf says:
>
> Program editconf, VERSION 4.5.4
> Source code file: pdbio.c, line: 446
>
> Software inconsistency error:
> Trying to deduce atomnumbers when no pdb information is present
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> What would be the correct format of pdb that is readable? Here is the pdb:
>

Google "PDB format."

-Justin

> 1Eth    1  C                   0.672  -0.000   0.000
> C
> 1Eth    2  C                  -0.672  -0.000   0.000
> C
> 1Eth    3  H                   1.238  -0.928   0.000
> H
> 1Eth    4  H                   1.238   0.928   0.000
> H
> 1Eth    5  H                  -1.238  -0.928   0.000
> H
> 1Eth    6  H                  -1.238   0.928   0.000
> H
>
> Thanks
>
>
>
> On 1 April 2013 20:06, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 4/1/13 7:22 PM, Juliette N. wrote:
>>
>>> Hi all,
>>>
>>> I am trying to produce gro file from PDB file using editconf.
>>>
>>> Here is the pdb file
>>>
>>> HETATM    1  C                   0.672  -0.000
>>> 0.000                       C
>>> HETATM    2  C                  -0.672  -0.000
>>> 0.000                       C
>>> HETATM    3  H                   1.238  -0.928
>>> 0.000                       H
>>> HETATM    4  H                   1.238   0.928
>>> 0.000                       H
>>> HETATM    5  H                  -1.238  -0.928
>>> 0.000                       H
>>> HETATM    6  H                  -1.238   0.928
>>> 0.000                       H
>>>
>>> Then I use: editconf -f X.pdb -o X.gro
>>>
>>> But the go file seems no to be correct
>>>
>>>       6
>>>       0         C    1   0.067  -0.000   0.000
>>>       0         C    2  -0.067  -0.000   0.000
>>>       0         H    3   0.124  -0.093   0.000
>>>       0         H    4   0.124   0.093   0.000
>>>       0         H    5  -0.124  -0.093   0.000
>>>       0         H    6  -0.124   0.093   0.000
>>>      0.00000   0.00000   0.00000
>>>
>>> Can anyone please help why this is happening?
>>>
>>>
>> And what exactly is wrong with it?  You have no residue numbers or names
>> in the input .pdb file, so none appear in the .gro file.  The coordinates
>> have been correctly transformed from Angstrom to nm within the limit of
>> precision.
>>
>> -Justin
>>
>> --
>> ==============================**==========
>>
>> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> * Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>
>
>
>

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

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

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