[gmx-users] Re: Internal water in the membrane receptor
Mark.Abraham at anu.edu.au
Mon Feb 27 10:07:14 CET 2012
On 27/02/2012 5:03 PM, James Starlight wrote:
> 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
> 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"
> 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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