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

[Emine Deniz Tekin]

Hi Justin,


Thank you for your reply.


Before I contacted you and do what you suggested , I did the following way:
1)      Firstly, I created the lipopetide (12 Carbon atoms (tail) +
Val-Val-Ala-Gly-Glu-Arg-Gly-Asp) using ChemDraw and saved as a PDB. 2)
     Then,
I pasted my pdb file to the The Dundee PRODRG2.5 Server (beta) and I got
conf.gro and topol.top files. 3)      After completing some of the missing
information by hand at the topology file (e.g  #include
"gromos53a6.ff/forcefield.itp"..), started the simulation for 10 ns. Simulation
went through without an apparent error. But I saw that when I watch the
trajectory at Visual Molecular Dynamics (VMD), some bonds seem much longer
than they should be. What could be the reason for this? I wonder  if
something ‘s wrong in the above process.

Thank you in advance,



Deniz



On Wed, Feb 23, 2011 at 3:57 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Emine Deniz Tekin wrote:
>
>>
>> Hi gromacs users,
>>
>>
>> I am using the gromacs 4.5.3 version. I created a lipopetide which consist
>> of 12 Carbon atoms (tail) connected to Val-Val-Ala-Gly-Glu-Arg-Gly-Asp
>> (residues) using ARGUSLAB and I saved it as a pdb file.
>>
>> Then, when I used the following command in gromacs:
>>
>>  pdb2gmx   –f    lipopepArgus.pdb    (GROMOS96 45a3 force field&spc type
>> water model)
>>
>>  I got the following error message:
>>
>>  Fatal error:
>>
>> Residue 'DEF' not found in residue topology database
>>
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>>
>> website at http://www.gromacs.org/Documentation/Errors
>>
>>
>> As far as I could understand, there is no problem with the residues  but
>>  there is a problem with the atoms in the tail (12 Carbon atoms, 23 Hydrogen
>> atoms and an Oxygen atom, actually it is called a lauroic acid). These atoms
>> are defined as DEF.  I thought  I should  rename the pdb to the expected
>> name given in the .rtp file of  the 45a3 force field for my lipopeptide. But
>> I could not find a parameterization for the  lauroic acid. In this case,
>> what shoul I do?
>>
>>
>> At the
>> http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blockspage, I found;
>>
>>
>> *Abbrev.*
>>
>>
>>
>> *Source*
>>
>>
>>
>> *2*
>>
>>
>>
>> *Full Name*
>>
>>
>>
>> *Formula*
>>
>>
>>
>> *Specifics*
>>
>> LAU
>>
>>
>>
>> fa.itp
>>
>>
>>
>> O
>>
>>
>>
>> lauroic acid
>>
>>
>>
>> C_11 H_23 COOH
>>
>>
>>
>>
>> -
>>
>>
>> Does using fa.itp file solve my problem? If yes, where can I get this
>> file?
>>
>>
>>
> This topology is from the deprecated Gromos87 (hacked) force field called
> ffgmx.  Don't use it.  The reasons are described in the manual.  What's
> more, you can't use a standalone topology if your molecule is covalently
> linked to a peptide.  You can't have bonds between different [moleculetypes]
> (i.e. between topologies) in Gromacs.
>
> The proper procedure is to parameterize the lauroic acid:
>
> http://www.gromacs.org/Documentation/How-tos/Parameterization
>
> or obtain compatible parameters from elsewhere and implement them in your
> chosen force field:
>
>
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>
> You could use Berger lipid parameters for the lauroic acid moiety, you'll
> just have to add this residue to the force field.  The membrane protein
> tutorial I wrote will walk you through how to modify the force field
> properly.
>
> http://www.gromacs.org/Documentation/Tutorials#Membrane_Simulations
>
> -Justin
>
>
>  I would be so glad if you can help me solve this problem.
>> Thank you in advance,
>>
>> Deniz
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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