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

[Mark Abraham]

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

http://www.gromacs.org/Documentation/errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_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.

Mark

>
> 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
>
>
>
>

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