On 3/21/13 4:29 AM, neeru sharma wrote:
Message: 6
Date: Wed, 20 Mar 2013 09:04:05 -0400
From: Justin Lemkul <[email protected]>
Subject: Re: [gmx-users] Restraining water molecule
To: Discussion list for GROMACS users <[email protected]>
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On Wed, Mar 20, 2013 at 8:57 AM, neeru sharma <[email protected]
wrote:
Dear gromacs users,
I am simulating a system of Protein-ion-GTP with One Water molecule. I
want
to restrain this system (along with this water molecule) for minimization
and equilibration.
Everytime I run this by specifying the .itp files, it gives the error of
misplacement as follows:
*"This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right
molecule."
*
The sequence I am giving in the topology file is like this:
*
; Include Position restraint file for Protein-ion-GTP-Water
#ifdef POSRES_LIGAND
#include "posre_comp.itp"
#endif
; Include ligand topology
#include "gtp.itp"
; Include water topology
#include "gromos43a1.ff/spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "gromos43a1.ff/ions.itp"*
*
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein 1
GTP 1
SOL 1
SOL 12179
NA 8
*
Can anybody help me figuring out the issue,where I am doing wrong? Any
suggestion is welcome
If you want to restrain a single water molecule, it needs to be defined as
its own [moleculetype] or as a part of the protein [moleculetype]. Breaking
apart a continuous block of water causes problems with the SETTLE
algorithm, so you will need to manually specify three constraints (OW-HW1,
OW-HW2, and HW1-HW2) for this water molecule, while the remaining bath of
solvent would be handled by SETTLE.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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End of gmx-users Digest, Vol 107, Issue 81
******************************************
I tried restraining the single water molecule by specifying the
Protein-Ion-GTP-Water as one index group. The itp file, I used for this
water molecule was as follows:
*[ moleculetype ]
; molname nrexcl
WAT 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
#ifndef HEAVY_H
1 O 1 WAT O 1 -0.82 15.99940
2 H 1 WAT H1 1 0.41 1.00800
3 H 1 WAT H2 1 0.41 1.00800
#else
1 O 1 WAT O 1 -0.82 9.95140
2 H 1 WAT H1 1 0.41 4.03200
3 H 1 WAT H2 1 0.41 4.03200
#endif
#ifndef FLEXIBLE
[ settles ]
; O funct doh dhh
1 1 0.1 0.16330
[ exclusions ]
1 2 3
2 1 3
3 1 2
#else
[ bonds ]
; i j funct length force.c.
1 2 1 0.1 345000 0.1 345000
1 3 1 0.1 345000 0.1 345000
[ angles ]
; i j k funct angle force.c.
2 1 3 1 109.47 383 109.47 383
#endif*
But, ended with the fatal error:
*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.*
Then, I tried removed the settles block:
*[ settles ]
; O funct doh dhh
1 1 0.1 0.16330
*from the itp file. It then, ran the minimization steps which continued for
40 steps. But when I visualized the gro file generated, the conformation
and orientation of this particular water molecule was not proper. I feel, I
the settle section of itp file was not treated properly.
Any suggestion how to treat this water molecule?
Yes, read my post again. I already said this would happen and described exactly
what you have to do.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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