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On 27/02/2012 5:03 PM, James Starlight wrote:
<blockquote
cite="mid:CAALQopwbn4+uonV3tU0jbN3yxg4dnPr65qqs92DadZ1Pxxzitw@mail.gmail.com"
type="cite">Justin,<br>
<br>
<div class="gmail_quote">2012/2/25 Justin A. Lemkul <span
dir="ltr"><<a moz-do-not-send="true"
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>
<br>
<br>
</div>
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 </div>
</div>
</blockquote>
<br>
No. There's a numbering *within* a [moleculetype]. Your
[position_restraints] must be numbers in that range. The contents of
the .gro file are irrelevant to the correct interpretation of
[position_restraints]. The contents of the .gro file matters only
inasmuch as the ordering in your [molecules] section (and the
[atoms] sections it references) must match it.<br>
<br>
<blockquote
cite="mid:CAALQopwbn4+uonV3tU0jbN3yxg4dnPr65qqs92DadZ1Pxxzitw@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div>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>
</div>
</div>
</blockquote>
<br>
You've shuffled the chapters in the book, but this doesn't help you
find the 10th word in the chapter about the X-ray waters. (Yes, I
realise my analogy is not perfect...)<br>
<br>
Mark<br>
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