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<div class="gmail_quote">On Tue, Nov 1, 2011 at 5:44 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"><br><br>Steven Neumann wrote:
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<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"><br><br>On Tue, Nov 1, 2011 at 4:11 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br><br><br> Steven Neumann wrote:<br><br> Hi Guys,<br> I am using Charmm27 ff for my protein and ligand system. I used<br> SwissParam to generate the topology for my ligand. I included<br> the obtained topology of my ligand as in Justin tutorial:<br>
; Include Position restraint file<br><br> #ifdef POSRES<br><br> #include "posre.itp"<br><br> #endif<br><br> ; Include ligand topology<br><br> #include "ligand.itp"<br>
<br> ; Ligand position restraints<br><br> #ifdef POSRES<br><br> #include "posre_ligand.itp"<br><br> #endif<br><br> ; Include water topology<br><br> #include "charmm27.ff/tip3p.itp"<br>
<br> When I wanted to run NVT I obtained:<br> Fatal error:<br> Syntax error - File egcg.itp, line 7<br> Last line read:<br> '[ atomtypes ] '<br> Invalid order for directive atomtypes<br>
However when I included my topology as:<br> ; Include forcefield parameters<br><br> #include "charmm27.ff/forcefield.itp"<br><br> #include "ligand.itp"<br><br> [ moleculetype ]<br>
<br> ; Name nrexc<br><br> ......................<br><br> ; Include Position restraint file<br><br> #ifdef POSRES<br><br> #include "posre.itp"<br><br> #endif<br><br> ; Ligand position restraints<br>
<br> #ifdef POSRES<br><br> #include "posre_egcg.itp"<br><br> #endif<br><br> ; Include water topology<br><br> #include "charmm27.ff/tip3p.itp"<br><br> ,,,,<br> Everything seems to be ok!<br>
Any clue why is that?<br> <br><br> The topology must follow a defined order. Please consult Chapter 5<br> of the manual for the required hierarchy. Of course, the latter<br> case will also not work, because you've introduced ligand position<br>
restraints after the protein [moleculetype], so if invoked, they<br> will cause a different fatal error.<br><br> The Gromacs site also has more on these types of errors, as well as<br> the list archive, where this error has been posted and solved<br>
hundreds of times.<br><br> -Justin<br><br> Thank you Justin! But actually the last case I provided actually<br> works...<br><br></blockquote><br></div></div>Then the position restraints are not being applied to the ligand. They can't be. Once the protein [moleculetype] is introduced, all [position_restraints] directives immediately after are applied to it. Try invoking the restraints separately, i.e. with "define = -DPOSRES -DPOSRES_LIGAND" and you will get a fatal error.
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<div class="h5"><br><br>-Justin</div></div></blockquote>
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<div>You are as always right :) Thanks!</div>
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<div>Steven</div></div>