On 9/6/13 5:27 PM, Rama Krishna Koppisetti wrote:
Sorry ..,here are my distance restraints file:
Without context as to what these numbers are, there's little useful information
here. I suspect you're trying to implement restraints between protein and lipid
atoms, which will not work for reasons described in my last mail.
-Justin
[ distance_restraints ]
; ai aj type index type' low
up1 up2 fac
301 2679 1 0 1 0.0
1.6214 2.211 1.0
301 2696 1 0 1 0.0
1.6214 2.211 1.0
301 3415 1 0 1 0.0
1.6214 2.211 1.0
301 3432 1 0 1 0.0
1.6214 2.211 1.0
301 6635 1 0 1 0.0
1.6214 2.211 1.0
301 6652 1 0 1 0.0
1.6214 2.211 1.0
301 7187 1 0 1 0.0
1.6214 2.211 1.0
301 7204 1 0 1 0.0
1.6214 2.211 1.0
301 7279 1 0 1 0.0
1.6214 2.211 1.0
301 7296 1 0 1 0.0
1.6214 2.211 1.0
301 7371 1 0 1 0.0
1.6214 2.211 1.0
301 7388 1 0 1 0.0
1.6214 2.211 1.0
301 7923 1 0 1 0.0
1.6214 2.211 1.0
301 7940 1 0 1 0.0
1.6214 2.211 1.0
301 8199 1 0 1 0.0
1.6214 2.211 1.0
301 8216 1 0 1 0.0
1.6214 2.211 1.0
344 2679 1 1 1 0.0
1.5763 2.1495 1.0
344 2696 1 1 1 0.0
1.5763 2.1495 1.0
344 3415 1 1 1 0.0
1.5763 2.1495 1.0
344 3432 1 1 1 0.0
1.5763 2.1495 1.0
344 6635 1 1 1 0.0
1.5763 2.1495 1.0
344 6652 1 1 1 0.0
1.5763 2.1495 1.0
344 7187 1 1 1 0.0
1.5763 2.1495 1.0
344 7204 1 1 1 0.0
1.5763 2.1495 1.0
344 7279 1 1 1 0.0
1.5763 2.1495 1.0
344 7296 1 1 1 0.0
1.5763 2.1495 1.0
344 7371 1 1 1 0.0
1.5763 2.1495 1.0
344 7388 1 1 1 0.0
1.5763 2.1495 1.0
344 7923 1 1 1 0.0
1.5763 2.1495 1.0
344 7940 1 1 1 0.0
1.5763 2.1495 1.0
344 8199 1 1 1 0.0
1.5763 2.1495 1.0
344 8216 1 1 1 0.0
1.5763 2.1495 1.0
889 2679 1 2 1 0.0
1.8304 2.496 1.0
889 2696 1 2 1 0.0
1.8304 2.496 1.0
889 3415 1 2 1 0.0
1.8304 2.496 1.0
889 3432 1 2 1 0.0
1.8304 2.496 1.0
889 6635 1 2 1 0.0
1.8304 2.496 1.0
889 6652 1 2 1 0.0
1.8304 2.496 1.0
889 7187 1 2 1 0.0
1.8304 2.496 1.0
889 7204 1 2 1 0.0
1.8304 2.496 1.0
889 7279 1 2 1 0.0
1.8304 2.496 1.0
889 7296 1 2 1 0.0
1.8304 2.496 1.0
889 7371 1 2 1 0.0
1.8304 2.496 1.0
889 7388 1 2 1 0.0
1.8304 2.496 1.0
889 7923 1 2 1 0.0
1.8304 2.496 1.0
889 7940 1 2 1 0.0
1.8304 2.496 1.0
889 8199 1 2 1 0.0
1.8304 2.496 1.0
889 8216 1 2 1 0.0
1.8304 2.496 1.0
922 2679 1 3 1 0.0
1.5433 2.1045 1.0
922 2696 1 3 1 0.0
1.5433 2.1045 1.0
922 3415 1 3 1 0.0
1.5433 2.1045 1.0
922 3432 1 3 1 0.0
1.5433 2.1045 1.0
922 6635 1 3 1 0.0
1.5433 2.1045 1.0
922 6652 1 3 1 0.0
1.5433 2.1045 1.0
922 7187 1 3 1 0.0
1.5433 2.1045 1.0
922 7204 1 3 1 0.0
1.5433 2.1045 1.0
922 7279 1 3 1 0.0
1.5433 2.1045 1.0
922 7296 1 3 1 0.0
1.5433 2.1045 1.0
922 7371 1 3 1 0.0
1.5433 2.1045 1.0
922 7388 1 3 1 0.0
1.5433 2.1045 1.0
922 7923 1 3 1 0.0
1.5433 2.1045 1.0
922 7940 1 3 1 0.0
1.5433 2.1045 1.0
922 8199 1 3 1 0.0
1.5433 2.1045 1.0
922 8216 1 3 1 0.0
1.5433 2.1045 1.0
1113 2679 1 4 1 0.0
1.5906 2.169 1.0
1113 2696 1 4 1 0.0
1.5906 2.169 1.0
1113 3415 1 4 1 0.0
1.5906 2.169 1.0
1113 3432 1 4 1 0.0
1.5906 2.169 1.0
1113 6635 1 4 1 0.0
1.5906 2.169 1.0
1113 6652 1 4 1 0.0
1.5906 2.169 1.0
1113 7187 1 4 1 0.0
1.5906 2.169 1.0
1113 7204 1 4 1 0.0
1.5906 2.169 1.0
1113 7279 1 4 1 0.0
1.5906 2.169 1.0
1113 7296 1 4 1 0.0
1.5906 2.169 1.0
1113 7371 1 4 1 0.0
1.5906 2.169 1.0
1113 7388 1 4 1 0.0
1.5906 2.169 1.0
1113 7923 1 4 1 0.0
1.5906 2.169 1.0
1113 7940 1 4 1 0.0
1.5906 2.169 1.0
1113 8199 1 4 1 0.0
1.5906 2.169 1.0
1113 8216 1 4 1 0.0
1.5906 2.169 1.0
1123 2679 1 5 1 0.0
1.7985 2.4525 1.0
1123 2696 1 5 1 0.0
1.7985 2.4525 1.0
1123 3415 1 5 1 0.0
1.7985 2.4525 1.0
1123 3432 1 5 1 0.0
1.7985 2.4525 1.0
1123 6635 1 5 1 0.0
1.7985 2.4525 1.0
1123 6652 1 5 1 0.0
1.7985 2.4525 1.0
1123 7187 1 5 1 0.0
1.7985 2.4525 1.0
1123 7204 1 5 1 0.0
1.7985 2.4525 1.0
1123 7279 1 5 1 0.0
1.7985 2.4525 1.0
1123 7296 1 5 1 0.0
1.7985 2.4525 1.0
1123 7371 1 5 1 0.0
1.7985 2.4525 1.0
1123 7388 1 5 1 0.0
1.7985 2.4525 1.0
1123 7923 1 5 1 0.0
1.7985 2.4525 1.0
1123 7940 1 5 1 0.0
1.7985 2.4525 1.0
1123 8199 1 5 1 0.0
1.7985 2.4525 1.0
1123 8216 1 5 1 0.0
1.7985 2.4525 1.0
1148 2679 1 6 1 0.0
1.5169 2.0685 1.0
1148 2696 1 6 1 0.0
1.5169 2.0685 1.0
1148 3415 1 6 1 0.0
1.5169 2.0685 1.0
1148 3432 1 6 1 0.0
1.5169 2.0685 1.0
1148 6635 1 6 1 0.0
1.5169 2.0685 1.0
1148 6652 1 6 1 0.0
1.5169 2.0685 1.0
1148 7187 1 6 1 0.0
1.5169 2.0685 1.0
1148 7204 1 6 1 0.0
1.5169 2.0685 1.0
1148 7279 1 6 1 0.0
1.5169 2.0685 1.0
1148 7296 1 6 1 0.0
1.5169 2.0685 1.0
1148 7371 1 6 1 0.0
1.5169 2.0685 1.0
1148 7388 1 6 1 0.0
1.5169 2.0685 1.0
1148 7923 1 6 1 0.0
1.5169 2.0685 1.0
1148 7940 1 6 1 0.0
1.5169 2.0685 1.0
1148 8199 1 6 1 0.0
1.5169 2.0685 1.0
1148 8216 1 6 1 0.0
1.5169 2.0685 1.0
1418 2679 1 7 1 0.0
1.562 2.130 1.0
1418 2696 1 7 1 0.0
1.562 2.130 1.0
1418 3415 1 7 1 0.0
1.562 2.130 1.0
1418 3432 1 7 1 0.0
1.562 2.130 1.0
1418 6635 1 7 1 0.0
1.562 2.130 1.0
1418 6652 1 7 1 0.0
1.562 2.130 1.0
1418 7187 1 7 1 0.0
1.562 2.130 1.0
1418 7204 1 7 1 0.0
1.562 2.130 1.0
1418 7279 1 7 1 0.0
1.562 2.130 1.0
1418 7296 1 7 1 0.0
1.562 2.130 1.0
1418 7371 1 7 1 0.0
1.562 2.130 1.0
1418 7388 1 7 1 0.0
1.562 2.130 1.0
1418 7923 1 7 1 0.0
1.562 2.130 1.0
1418 7940 1 7 1 0.0
1.562 2.130 1.0
1418 8199 1 7 1 0.0
1.562 2.130 1.0
1418 8216 1 7 1 0.0
1.562 2.130 1.0
1425 2679 1 8 1 0.0
1.5246 2.079 1.0
1425 2696 1 8 1 0.0
1.5246 2.079 1.0
1425 3415 1 8 1 0.0
1.5246 2.079 1.0
1425 3432 1 8 1 0.0
1.5246 2.079 1.0
1425 6635 1 8 1 0.0
1.5246 2.079 1.0
1425 6652 1 8 1 0.0
1.5246 2.079 1.0
1425 7187 1 8 1 0.0
1.5246 2.079 1.0
1425 7204 1 8 1 0.0
1.5246 2.079 1.0
1425 7279 1 8 1 0.0
1.5246 2.079 1.0
1425 7296 1 8 1 0.0
1.5246 2.079 1.0
1425 7371 1 8 1 0.0
1.5246 2.079 1.0
1425 7388 1 8 1 0.0
1.5246 2.079 1.0
1425 7923 1 8 1 0.0
1.5246 2.079 1.0
1425 7940 1 8 1 0.0
1.5246 2.079 1.0
1425 8199 1 8 1 0.0
1.5246 2.079 1.0
1425 8216 1 8 1 0.0
1.5246 2.079 1.0
On Fri, Sep 6, 2013 at 4:23 PM, Rama <ramkishn...@gmail.com> 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)./
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
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==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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