[gmx-users] questions on distance restraints

NG HUI WEN HuiWen.Ng at nottingham.edu.my
Wed Jan 18 01:30:08 CET 2012

Dear gmxusers,

I have some questions about distance restraints that I hope you would be able to shed some light on. Thanks in advance.

I am trying to apply distance restraints to my protein. Below was what I did:

-use genrestr to create my ca_disre.itp
genrestr -f membedded_em.gro -o ca_disre.itp -disre (pop-up prompt: CA atoms selected)

-in my mdp file
I added this line near the top:
define          = -DDISRES

-my  top file looks like that
; Include forcefield parameters
#include "gromos53a6_lipid.ff/forcefield.itp"

;Include Protein Topology
#include "A2a.itp"

; Include Position restraint file
#ifdef DISRES
#include "ca_disre.itp"
#ifdef POSRES
#include "posre.itp"

;Include POPC topology
#include "popc.itp"
#include "lipid_posre.itp"

;Include water topology
#include "gromos53a6_lipid.ff/spc.itp"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000

; Include topology for ions
#include "gromos53a6_lipid.ff/ions.itp"

[ system ]
; Name
Protein and POPC and Water

[ molecules ]
; Compound        #mols
Protein_chain_X     1
POPC              327
SOL         24767
CL          11

The simulation ran without a problem. However, after it was completed, I compared the final protein structure with the initial and it looked like the atoms (even the CA atoms , especially those in the loops) had moved quite a fair bit away from the original position. This made me wonder if the distance restraints had indeed been applied or perhaps the force constant was not large enough (default =1000 kJ/mol/nm^2)?  I had checked the mdout.mdp file "define  = -DDISRES" was there... wasn't sure how else I could check this.

To test whether it was due to the latter, I had tried rerunning the simulation for 1ns simulation with "disre_fc        = 10000" added to the mdp file. This time the atoms did not move as far away as previously observed.

I have tried google-ing for the proper way to impose distance restraints but didn't find my searches too useful. I wonder if anyone could confirm with me that the above method is correct/ tell me that I had done something wrong.

Cheers for that!

Best wishes,

<< This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. 

This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK & Malaysia legislation. >>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120118/5c6e55be/attachment.html>

More information about the gromacs.org_gmx-users mailing list