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

[reisingere at rostlab.informatik.tu-muenchen.de]

Thank you very much for this detailed answer!!

> 'pdb2gmx' is mainly a tool to get the topology for (bigger) molecules
> from a *.pdb file. 'pdbgmx' is expecting an entry in the *.rtp file for
> the dummy atoms. You could add one in that file... (see further below)
>
> But if the dummys only interact via nonbonded interactions it would be
> more convient to write the topology by hand.
> In the *.top file, you would need after the protein a new entry with
> [ moleculetype ]
> and
> [ atoms ]
> But you should also have this nonbonded interaction in the *nb.itp and
> file of your force field and the atom definition in the *.atp file.
>
>
> If there are also bonded parameters the new *.rtp entry would be better.
> For this look at the definition of an aminoacid, or a single molecule
> and write something similar for your dummy atoms.
> Essential you would need the atoms definitions and charges, and then an
> entry for which atoms is bonded to which.
>
> But you should also have these interactions (nonbonded and bonded) in
> the *nb.itp and *bon.itp files of your force field and the atom
> definition in the *.atp file.
>
> The basic informations for both ways are in chapter 5 of the manual.
>
> Hope this gives some hints.
> Greetings
> Thomas Schlesier
>
>
>
> Am 20.06.2012 16:18, schrieb gmx-users-request at gromacs.org:
>> 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.
>>
>>
>> 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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