[gmx-users] How to setup a system of a protein attached to a small molecule?

Mark Abraham Mark.Abraham at anu.edu.au
Mon Feb 6 18:45:46 CET 2012

On 7/02/2012 2:26 AM, Qinghua Liao wrote:
> Dear GMX users,
> We are trying to do a simulation of a protein attached to a small 
> molecules, how should I do to setup the system? For the parameters of 
> the small molecule, I got it from ATB sever, however I don't know how 
> to bond the small molecule and the N terminal of protein.

The general solution is to use 
http://www.gromacs.org/Documentation/File_Formats/specbond.dat to allow 
pdb2gmx to learn about the bond to the new molecule. As you will see in 
your [bonds] section, you have no bond to your new residue.

> For gro file, it is ok, but for the topology file, I tried to merge 
> the parameters of small molecule and the topology file together, and 
> then renumber the atom number, and the grompp worked. But when I 
> wanted to do the geometry optimization, it did not work. Here is the 
> error:
> Fatal error:
> There is no domain decomposition for 4 nodes that is compatible with 
> the given box and a minimum cell size of 3.52902 nm


You have set up your "small" molecule with only three charge groups. 
mdrun functions as a large number of loops over interactions between and 
within charge groups. The size of your large charge groups creates a 
large lower bound on the number of atoms that have to be present on each 
processor of a parallel simulation, and your number of molecules is 
unsuitable for this. You need to investigate how to generate charge 
groups that are both smaller and consistent with the force field.


> I guess it is still a problem of the setup of the system, the 
> attachments are the gro and top files for the system. So could someone 
> give me some suggestions? Thanks very much!
> -- 
> Best Regards,
> Qinghua

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120207/2b0c3d7b/attachment.html>

More information about the gromacs.org_gmx-users mailing list