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.
Mark
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