[gmx-users] NMR restrained MD

[Justin Lemkul]

On 9/6/13 5:23 PM, Rama wrote:
> 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)./
>

Just like position restraints, distance restraints only work within a 
[moleculetype].  Thus you're probably trying to restrain atoms between 
[moleculetype] directives, which does not work.  You could theoretically make a 
merged [moleculetype] of whatever species need to be restrained, but that may 
take a bit of effort depending on what is being restrained.

-Justin

> 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.
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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