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

[Justin A. Lemkul]

On 6/20/12 12:13 PM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> With the *nb.itp file you ment the "ffnonbonded.itp" file, right?
>

Yes.  Thomas was referring to the old nomenclature of force field files.

> But there is one thing:
> Of course you are right, I can modify the .top file and add my Dummy atom
> there. But because I got this error I mentioned, the pdb2gmx didn't
> produce a .gro file.
>

pdb2gmx is not generally suited for dealing with complex systems, though in some 
cases it does work.  It is for this reason that one does not typically provide, 
for instance, a protein in water with ions and some ligand to pdb2gmx.  You 
create the protein topology with pdb2gmx, and then add in whatever else is 
necessary (solvent, ions, other molecules) and simply #include their parameters 
using .itp files.

-Justin

> Bests, Eva
>
>
>> '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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>
>

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

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

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