[gmx-users] Re: Internal water in the membrane receptor

Mark Abraham Mark.Abraham at anu.edu.au
Mon Feb 27 10:07:14 CET 2012

On 27/02/2012 5:03 PM, James Starlight wrote:
> Justin,
> 2012/2/25 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>     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.
> Yes, this works! Thanks alot.
> I only wounder to know should I delete
> [ 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.
>     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].
> It's clear now. As I understtod the  [moleculetype] of the restricted 
> molecule must be in FIRST place in my topol.top

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.

> 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
> ; Include X-ray water topology
> #include "XW.itp"
> ; Include Position restraint for XW
> #ifdef POSRES_XW
> #include "posre_XW.itp"
> #endif
> at the begining of the topol.top file. But the error during grompt was 
> the same about wrong atom order :(

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...)

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