Today I've tried to model internal water and forced with some problems :)<br><br>I've built my system by transferring water from X-ray structure to my model. Than I've minimized this new structure in vacuum and water still present on the desired positions<br>
<br>1) But when I've made my complete system ( with membrane mimicking Ccl4 layer) I've obtained this strange error during MDrun of this whole system ( there are no any errors during gromp pre-processing)<br><br>Fatal error:<br>
The [molecules] section of your topology specifies more than one block of<br>a [moleculetype] with a [settles] block. Only one such is allowed. If you<br>are trying to partition your solvent into different *groups* (e.g. for<br>
freezing, T-coupling, etc.) then you are using the wrong approach. Index<br>files specify groups. Otherwise, you may wish to change the least-used<br>block of molecules with SETTLE constraints into 3 normal constraints.<br>
<br><br>My topology has the below constracton<br><br>[ molecules ]<br>; Compound #mols<br>Protein 1<br>XW 16<br>Ccl4 804<br>SOL 9884<br><br>where XW is the new .itp made for internal water based on SPC.itp <br>
<br>I dont know what exactly this strange error means and how to fix it :(<br><br><br>2) Also when I've changed protonation state of two ASP residues all internal water left protein interior diffusing in the interiour during in vacuum minimisation :)<br>
I've tried to apply POSRES of that internal water but another eror occur<br><br>[ file posre_XW.itp, line 5 ]:<br>Atom index (4229) in position_restraints out of bounds (1-3).<br>This probably means that you have inserted topology section "position_restraints"<br>
<br>I've checked posre_XW.itp file and didnt find any errors! The atom numbers in posres are correspond to the atom nymbers in the GRO file. Why this error might occur?<br><br>my topology<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>my mdp<br>define = -DPOSRES_XW<br>integrator = steep<br><br>James<br>
<br><div class="gmail_quote">2012/2/25 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im">On 25/02/2012 5:37 AM, James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Mark,<br>
<br>
<br>
So as I understood the ussage of X-ray structure as the starting model where the internal water is already present might be good in case to avoid those sterric issues doesn't it ?<br>
</blockquote>
<br></div>
Yes. This was one of the options I suggested earlier.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
What are additional options should I use for preparation of such system with pdb2gmx ? Should I use posres on the internal water ( e.g on oxygen atoms) during energy minimisation and equilibration phases?<br>
</blockquote>
<br></div>
You probably do want a contiguous block of atoms with position restraints. That will require you have two different [moleculetype] sections for the different "kinds" of water, since the [position_restraints] section applies to all instances of its [moleculetype], and you will need to disable [settle] for at least one of those. It might be easier not to use separate restraints for a subset of water.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span><div class="HOEnZb"><div class="h5"><br>
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