Thanks<br><br><div class="gmail_quote">On Fri, Mar 16, 2012 at 10:37 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"><div class="im">
On 17/03/2012 12:39 AM, Anthony Cruz Balberdi wrote:
<blockquote type="cite">
<div class="gmail_quote"><br>
On Wed, Mar 14, 2012 at 8:42 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div>On 15/03/2012 5:33 AM, Anthony Cruz Balberdi
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Users:<br>
<br>
I was trying to calculate the energy contribution of an
specific ion in my simulation. After extract a given
frame from the simulation, I recalculate the energies of
this frame with mdrun -rerun. Then I used tpbconv and
editconf to create a new gro file and a new tpr without
the ion. I tried to run mdrun -rerun with this new files
but the mdrun stops with the following error:<br>
<br>
Program mdrun, VERSION 4.5.5<br>
Source code file: domdec_top.c, line: 744<br>
<br>
Software inconsistency error:<br>
Not enough position restraint coordinates<br>
<br>
What could be the problem?<br>
</blockquote>
<br>
</div>
</div>
Probably some [moleculetype] now has insufficient atoms to
cope with its position restraints, which apparently weren't
edited (correctly) by the tpbconv subset procedure.<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Any possible solution?<br>
</blockquote>
<br>
Probably depends on your use of position restraints, which
would have been a good thing to have included in your original
post....<span></span></blockquote>
<div><br>
Thank for your answer and sorry for the missing information.
The position restraint is acting on the protein backbone.
Since has nothing to do with the ion, I dont understand why
the error... <br>
<br>
Anthony<br>
</div>
<br>
</div>
</blockquote>
<font color="#888888"><br>
</font></div><font color="#888888">OK, so maybe tpbconv subsets don't work
well with position restraints. You can probably do what you want
with a suitable combination of energy groups and mdrun -rerun.</font><span class="HOEnZb"><font color="#888888"><br>
<br>
Mark<br>
<font color="#888888"></font>
</font></span></div>
<br>--<br>
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