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

Qinghua Liao fantasticqhl at gmail.com
Mon Feb 6 16:26:48 CET 2012

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. 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

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,

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