[gmx-users] Labeled protein

[Justin A. Lemkul]

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

-Justin

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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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