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

James Starlight jmsstarlight at gmail.com
Sat Feb 25 18:07:04 CET 2012

Today I've tried to model internal water and forced with some problems :)

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

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)

Fatal error:
The [molecules] section of your topology specifies more than one block of
a [moleculetype] with a [settles] block. Only one such is allowed. If you
are trying to partition your solvent into different *groups* (e.g. for
freezing, T-coupling, etc.) then you are using the wrong approach. Index
files specify groups. Otherwise, you may wish to change the least-used
block of molecules with SETTLE constraints into 3 normal constraints.

My topology has the below constracton

[ molecules ]
; Compound        #mols
Protein             1
XW                  16
Ccl4                804
SOL                 9884

where XW is the new .itp made for internal water based on SPC.itp

I dont know what exactly this strange error means and how to fix it :(

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 :)
I've tried to apply POSRES of that internal water but another eror occur

[ file posre_XW.itp, line 5 ]:
Atom index (4229) in position_restraints out of bounds (1-3).
This probably means that you have inserted topology section

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?

my topology
; Include X-ray water topology
#include "XW.itp"

; Include Position restraint for XW
#ifdef POSRES_XW
#include "posre_XW.itp"

my mdp
define        = -DPOSRES_XW
integrator    = steep


2012/2/25 Mark Abraham <Mark.Abraham at anu.edu.au>

> On 25/02/2012 5:37 AM, James Starlight wrote:
>> Mark,
>> 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 ?
> Yes. This was one of the options I suggested earlier.
>> 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?
> 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.
> Mark
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