[gmx-users] editconf- pdb to gro format

[Juliette N.]

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:

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>
>



-- 
Thanks,
J. N.