<br>
shiva birgani wrote:<br>
> Dear Justin<br>
> I have prepared the pdb structure of an organic compound.<br>
> This compound is applied as a lable which covalently and specifically<br>
> attaches to a Cys residue of our protein.<br>
> I want to attache the label to the protein and simulate this complex.<br>
> what I need to know is that Can I manualy attache the lable o the<br>
> protein in the primary pdb file of protein or the other way is<br>
> suggested? If there are other points that I should concern in this<br>
> regard?<br>
><br>
<br>
The molecule must be present in the starting .pdb file. For any new species<br>
that you need to introduce, you will first have to develop reasonable force<br>
field parameters for it (an advanced topic, beware), then construct the<br>
appropriate building blocks.<br>
<br>
<a href="http://www.gromacs.org/Documentation/How-tos/Parameterization" target="_blank">http://www.gromacs.org/Documentation/How-tos/Parameterization</a><br>
<a href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field" target="_blank">http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</a><br>
<br>
Dear Justin<br>Regarding to developing the reasonable force field parameters is not a small work, I would like to know your opinion about using <font size="2">PRODRG2.5 Server.<br><br>Thanks<br>Shiva<br></font>