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

[Justin A. Lemkul]

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
>

-- 
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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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