[gmx-users] How to setup a system of a protein attached to a small molecule?
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
> 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,
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users