<div class="gmail_quote">Dear GMX users,<div><br></div><div>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:</div>
<div><br></div><div> <br clear="all"><div><div>Fatal error:</div><div>There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 3.52902 nm</div></div><div><br></div><div>
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!</div><span><font color="#888888"><div>
<br></div><div><br></div></font></span></div></div><br clear="all"><div><br></div>-- <br>Best Regards,<div><br></div><div>Qinghua</div><div><br></div><br>