[gmx-users] NMR restrained MD

[Rama]

Hi,

I'm doing NMR restrained MD simulation for protein-Bilayer system to satisfy
NMR experimental data. 

Without restraints there is no problem, but if I include distance restraints
in topology file, getting fatal error:

the lipid atom index # was not recognized by using this command:
 g_grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
md.tpr -maxwarn 5

even in index file protein_DMPC atoms index is there continuously. Any one
have suggestions to overcome this fatal error. Thanks

/
[ file beta_disres.itp, line 4 ]:
Atom index (2679) in distance_restraints out of bounds (1-2513)./

md.mdp file:
title             =  protein-bilayer  complex
define          = -DDISRES      ; NMR Distance restraints
; Run parameters
integrator	= md		; leap-frog integrator
nsteps		= 2500000	; 
dt		    = 0.002		; 2 fs
; Output control
nstxout		= 5000		; save coordinates every 5 ps
nstvout		= 5000		; save velocities every 5 ps
nstxtcout	= 5000		; xtc compressed trajectory output every 5 ps
nstenergy	= 5000		; save energies every 5 ps
nstlog		= 5000		; update log file every 5 ps
; Bond parameters
continuation	= yes		    ; Restarting after NPT 
constraint_algorithm = lincs	; holonomic constraints 
constraints	= all-bonds	        ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter	= 1		            ; accuracy of LINCS
lincs_order	= 4		            ; also related to accuracy
; Distance restraints parameters
disre           = simple        ; simple (per-molecule) 
disre_fc        = 1000          ; force constant for distance restraints
; Neighborsearching
ns_type		= grid		; search neighboring grid cels
nstlist		= 5		    ; 10 fs
rlist		= 1.2		; short-range neighborlist cutoff (in nm)
rcoulomb	= 1.2		; short-range electrostatic cutoff (in nm)
rvdw		= 1.2		; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype	= PME		; Particle Mesh Ewald for long-range electrostatics
pme_order	= 4		    ; cubic interpolation
fourierspacing	= 0.16		; grid spacing for FFT
; Temperature coupling is on
tcoupl		= Nose-Hoover		    ; More accurate thermostat
tc-grps		= Protein     non-protein     non-protein	; three coupling groups -
more accurate
tau_t		=       0.5	 0.5       0.5	        ; time constant, in ps
ref_t		=       303	 303       303	        ; reference temperature, one for
each group, in K
; Pressure coupling is on
pcoupl		= Parrinello-Rahman	    ; Pressure coupling on in NPT
pcoupltype	= semiisotropic		    ; uniform scaling of x-y box vectors,
independent z
tau_p		= 2.0			        ; time constant, in ps
ref_p		= 1.0	1.0		        ; reference pressure, x-y, z (in bar)
compressibility = 4.5e-5	4.5e-5	; isothermal compressibility, bar^-1
; Periodic boundary conditions
pbc		    = xyz		; 3-D PBC
; Dispersion correction
DispCorr	= EnerPres	; account for cut-off vdW scheme
; Velocity generation
gen_vel		= no		; Velocity generation is off
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm         = 1
comm-mode       = Linear
comm-grps       = protein non-protein

topology file:


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

; Include Distance restraints file
#ifdef DISRES
#include "beta_disres.itp"
#endif

; Strong position restraints for InflateGRO
#ifdef STRONG_POSRES
#include "strong_posre.itp"
#endif

; Include DMPC topology
#include "ramaLJ.ff/dmpcLJ.itp"

; Include water topology
#include "ramaLJ.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 "ramaLJ.ff/ions.itp"

[ system ]
; Name
Giving Russians Opium May Alter Current Situation in water

[ molecules ]
; Compound        #mols
Protein                1
DMPC               125
SOL                8335
CL                     8         



--
View this message in context: http://gromacs.5086.x6.nabble.com/NMR-restrained-MD-tp5011025.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.