Justin,<br><br><div class="gmail_quote">2012/2/25 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im"><br>
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You likely have a [settles] directive applied the the XW molecules (crystal waters, yes?) and SOL. You can't do that. The block of molecules to which [settles] are applied must be continuous. You'll have to replace the [settles] directive in XW with normal constraints. <br>
</blockquote><div><br>Yes, this works! Thanks alot.<br>I only wounder to know should I delete<br>[ exclusions ] from the itp of my X-ray water or not ? This directive is linked with the [settles] by the if expression so I've replaced it too.<br>
</div><div> </div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="im"><br></div>
Your numbering is wrong. Numbering within a [position_restraints] directive has nothing to do with the .gro file, and is based on the numbering of the atoms in a [moleculetype].<br>
<br><br></blockquote><div>It's clear now. As I understtod the [moleculetype] of the restricted molecule must be in FIRST place in my topol.top file but in that file the PROTEIN at first place instead. How I could make this changing in my multi-topology file ? I've tried to place<br>
<br>; Include X-ray water topology<br>#include "XW.itp"<br><br>; Include Position restraint for XW<br>#ifdef POSRES_XW<br>#include "posre_XW.itp"<br>#endif<br><br>at the begining of the topol.top file. But the error during grompt was the same about wrong atom order :(<br>
<br><br>James<br></div></div><br>