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

Justin A. Lemkul jalemkul at vt.edu
Sat Feb 25 18:19:01 CET 2012

James Starlight wrote:
> 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 :(

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.  Mark already told you this in the last 

> 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 
> "position_restraints"
> 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?

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].


> my topology
> ; Include X-ray water topology
> #include "XW.itp"
> ; Include Position restraint for XW
> #ifdef POSRES_XW
> #include "posre_XW.itp"
> #endif
> my mdp
> define        = -DPOSRES_XW
> integrator    = steep
> James
> 2012/2/25 Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto: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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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