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

[Qinghua Liao]

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,

Qinghua
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120206/01984bed/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: groandtop.zip
Type: application/zip
Size: 23190 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120206/01984bed/attachment.zip>