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:
http://pubs.acs.org/doi/abs/10.1021/ci100335w
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
--
========================================
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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