[gmx-users] protein topology file with some substitutions by other founction groups

Mark Abraham Mark.Abraham at anu.edu.au
Thu Jul 9 06:10:21 CEST 2009

huifang liu wrote:
> Hello gmx-users,
> I want to run a system which contains about 200 amino acids. But i met 
> some problems with the topology file of this protein. Beacuse groups of 
> some residues are expected to be substituted by some other groups. For 
> example, the hydrogen atome of SH group in Cys is expected to be 
> substituted by -SH group to form a disulphur bond. So, Is there any one 
> who can teach me how to get a topology file of a protein like this?

You will need a thorough understanding of chapter 5 of the manual, and a 
working knowledge of setting up a "normal" simulation. You may need to 
edit the residue topology file (.rtp file) if you wish to use pdb2gmx.

Or you can start with a "normal" protein, run that through pdb2gmx and 
then edit the resulting .top file to correspond to the modified protein. 
Then you will need a coordinate file whose atomic ordering matches your 
.top file.

If your modified residues include functional groups that are not 
represented by the forcefield, then you have a much harder 
http://oldwiki.gromacs.org/index.php/Parameterization problem.


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