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

[Thomas Schlesier]

Yes, meant that file (didn't know the name for GMX 4.5.x, i use mainly 
4.0.7).

You can use:
editconf -f *.pdb -o *.gro
to convert the *.pdb file into a *.gro file. Since the *.gro file has 
only informations about:
atom names
residue name
coordinates
while the *.pdb has also additional informations.
Only problem could be the atom and residue names. But if i'm not 
mistaken, the *.pdb file needs the 'right' atom-names and residue names 
(the same atom names, which are also used in the *.rtp file) in order 
that 'pdb2gmx' can do its work (-> producing the *.top).

If you need the topology for the protein, you could delete all 
non-protein atoms and use 'pdb2gmx' to get it.
Then later write the data for the dummy atoms into the *.top.

But Justin hit an important point:
You need parameters for the
dummy - dummy
dummy - protein /  water
interactions, because GROMACS has none, and would give you the next error.
You can look into the literature if someone made parameters for this, 
probably you are lucky.
Else you need to determine the parameters yourself, which is not so 
easy. Again chapter 5 would be your friend for how force fields work. 
And looking into coarse-graining papers could be a good idea, since they 
do something similar.

Hope this helps
and wish you luck for finding / getting parameters.
Thomas


Am 20.06.2012 18:13, schrieb gmx-users-request at gromacs.org:
> With the *nb.itp file you ment the "ffnonbonded.itp" file, right?
>
> 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.
>
> 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, schriebgmx-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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