[gmx-users] Residue 'DUM' not found in residue topology database

Wed Jun 20 17:25:52 CEST 2012

Hi Justin,
yes I have already seen this site, but want I meant is that I have no idea
which values I should set. Is there something like a standard for dummy
protein for membrane?
Eva
>
>
> On 6/20/12 10:17 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>> Hi everybody,
>>
>> I try to use GROMACS for my protein where I added a layer of dummy atoms
>> simulating the membrane around it.
>> But now when I want to call "pdb2gmx" I always get the error:
>> Fatal error:
>> Residue 'DUM' not found in residue topology database
>> I understand the error, that there is no entry for the dummy residue in
>> the .tpr file. But is there a possibility to add it there. Because the
>> file don't look like that I can just write "DUM" in it.
>>
>>
>
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>
> -Justin
>
>> my pdb file looks like this:
>>
>> ATOM   2597  CB  LEU A 313      12.816 -29.877 -23.547  1.00 55.31
>>    C
>> ATOM   2598  CG  LEU A 313      14.261 -29.695 -23.059  1.00 54.06
>>    C
>> ATOM   2599  CD1 LEU A 313      15.169 -30.640 -23.866  1.00 53.26
>>    C
>> ATOM   2600  CD2 LEU A 313      14.757 -28.257 -23.179  1.00 54.46
>>    C
>> TER
>> HETATM 3076  DUM DUM A 314      -4.000 -49.000   6.000  1.00  1.70
>> HETATM 3077  DUM DUM A 314      -4.000 -49.000   7.000  1.00  1.70
>> HETATM 3078  DUM DUM A 314      -4.000 -48.000   6.000  1.00  1.70
>> HETATM 3079  DUM DUM A 314      -4.000 -48.000   7.000  1.00  1.70
>> .
>> .
>> .
>> .
>> HETATM 36213 O   HOH A 527      25.281 -35.299  13.147  1.00 37.03
>>    O
>> HETATM 36214 O   HOH A 528      46.452 -27.955 -20.733  1.00 19.63
>>    O
>> HETATM 36215 O   HOH A 530      32.439 -23.614 -26.720  1.00 27.12
>>    O
>> TER
>>
>>
>>
>>
>>
>>
>> Best regards,
>> Eva
>>
>
> --
> ========================================
>
> 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
>
> ========================================
>
>
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