[gmx-users] Labeled protein

Justin A. Lemkul jalemkul at vt.edu
Fri Jul 8 12:08:54 CEST 2011

shiva birgani wrote:
> shiva birgani wrote:
>  > Dear Justin
>  > I have prepared the pdb structure of an organic compound.
>  > This compound is applied as a lable which covalently and specifically
>  > attaches to a Cys residue of our protein.
>  > I want to attache the label to the protein and simulate this complex.
>  > what I need to know is that Can I manualy attache the lable o the
>  > protein in the primary pdb file of protein or the other way is
>  > suggested? If there are other points that I should concern in this
>  > regard?
>  >
> The molecule must be present in the starting .pdb file.  For any new species
> that you need to introduce, you will first have to develop reasonable force
> field parameters for it (an advanced topic, beware), then construct the
> appropriate building blocks.
> http://www.gromacs.org/Documentation/How-tos/Parameterization
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
> Dear Justin
> Regarding to developing the reasonable force field parameters is not a 
> small work, I would like to know your opinion about using PRODRG2.5 Server.

We recently published a paper detailing the problems with PRODRG:


That said, you can still use the topologies as a framework for further 
refinement, but I have never gotten sufficiently accurate parameters from PRODRG 
for even the simplest molecules.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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