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

[Justin A. Lemkul]

On 6/20/12 11:25 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> 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?

No.  You have to decide what these dummy atoms are and how they might (or might 
not) interact with the system and what parameters (if any) they have.  If 
they're completely non-interacting then there's not really any reason to have them.

-Justin

> 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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>
>
>

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

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

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