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
message.
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].
-Justin
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.abra...@anu.edu.au
<mailto:mark.abra...@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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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