I don't think the atom number is the problem. I also have systems with more than 99999 atoms, and in the gro file the atom number after 99999 is reset to 0, but that was never a problem for the simulations. I would check the parameters again, but I don't have a more exact answer to your problem.<br>
<br>
<div class="gmail_quote">2010/3/5 Carla Jamous <span dir="ltr"><<a href="mailto:carlajamous@gmail.com">carlajamous@gmail.com</a>></span><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Hi,<br>please I'm having a problem while running a minimisation.<br><br>I prepared my system with pdb2gmx and generated .pdb files. From the last pdb file, I did grompp & generated the tpr file that I used to start my minimization. At the 46th step, I encountered the problem:"water molecule cannot be settled".<br>
I looked at the pdb file and found that many water residues have the same number because above residue 9999, it restarts to count residue 0, 1, etc...<br><br>I prepared the same system but I generated .gro files instead of .pdb & started my minimization. But did't encounter the same problem.<br>
I looked at the gro file & here, it's the atomic number that can't be above 99999.<br><br>So did anyone encounter this problem before, & if yes, please do you have a solution to propose?<br><br>Thanks<br><font color="#888888"><br>
Carla<br><br></font><br>--<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br>