[gmx-users] help---How to define new residue in GROMACS?

Mark Abraham Mark.Abraham at anu.edu.au
Tue Aug 4 08:33:15 CEST 2009

¹ù½¨Â· wrote:
> My problem is How to define new residue in GROMACS?
> i have made a 3-d structure model for a protein based on a template protein£¬which has a heme group.
>    befor runing the gromacs molecular simulation,i must define the heme group as a new residue,How to define new residue in GROMACS?

You need both suitable parameters for your desired forcefield, and then 
to construct a correct topology. The required formats are described in 
chapter 5 of the manual. You would be well advised to get some 
experience in how the work-flow operates by running normal simulations 
on simple proteins, e.g. in tutorials.

If you wish to use pdb2gmx to create the topology, you will need to 
modify the residue topology file (.rtp) to add the new residue. 
http://oldwiki.gromacs.org/index.php/specbond.dat may also need to be 
changed to link the heme group properly.


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