[gmx-users] position restraints

[Shima Arasteh]

Yes sir!

What I have in my top file is :
; Include forcefield parameters
#include "./charmm36-modified.ff/forcefield.itp"


; Include chain topologies
#include "topol_Protein_chain_A.itp"
#ifdef POSRES
#include "protein_chain_A_posre.itp"
#endif
#include "topol_Protein_chain_B.itp"
#ifdef POSRES
#include "protein_chain_B_posre.itp"
#endif

; Include POPC chain topology
#include "popc.itp"
#ifdef POSRES_LIPID
#include "lipid_posre.itp"
#endif

; Include water topology
#include "./charmm36-modified.ff/tip3p.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 "./charmm36-modified.ff/ions.itp"

[ system ]
; Name
Protein

[ molecules ]
; Compound        #mols
Protein_chain_A     1
Protein_chain_B     1
POPC        238
SOL         18706
NA               615
CL               617


I used genrestr to create the itp file of P atom types.The generated itp file is lipid_posre.itp. If I need to send any other information please let me know.

 
Sincerely,
Shima


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Monday, March 25, 2013 10:13 PM
Subject: Re: [gmx-users] position restraints



On 3/25/13 1:40 PM, Shima Arasteh wrote:
> Believe me I add this line to mdp file as you wrote in KALP-15-DPPC.
> 

I believe what I see.  If you're trying to re-type from memory what's in your topology and/or .mdp file, that's not productive.  Please copy and paste to make efficient use of everyone's time.

> "define        = -DPOSRES_LIPID"
> 
> Also added these to top file.
> #ifdef POSRES_LIPID
> #include "lipid_posre.itp"
> #endif
>   But I get again this error that the "This probably means that you have inserted topology section "position_restraints"
> in a part belonging to a different molecule than you intended to."
> 
> Why this doesn't match?? I think POSITION RESTRAINING is making me crazy! :((
> Would you please help me?
> 

I've been trying, and it appears you're either giving inconsistent or incorrect information.  Copy and paste directly from your .top file whatever sections are relevant.  You also haven't said what is in lipid_posre.itp, which can be another source of problems.  You just said you've created it with genrestr, but you didn't say what group you included.  The numbering in the position restraint file is per [moleculetype], not the global atom numbering in the coordinate file.

-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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