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

James Starlight jmsstarlight at gmail.com
Mon Feb 27 07:03:43 CET 2012


2012/2/25 Justin A. Lemkul <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 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 :(

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