On 9/6/13 5:35 PM, Rama Krishna Koppisetti wrote:
H
i Justin,
Thanks for your reply.
How to do that?
If .rtp entries exist for your lipid with the force field, it's simply a matter
of pdb2gmx -merge, choosing which chains should be written as a single
[moleculetype]. If the lipids are not described by .rtp entries, you either
have to write one or modify the topology by hand (ugh) or with some script.
-Justin
On Fri, Sep 6, 2013 at 4:27 PM, Justin Lemkul <jalem...@vt.edu> wrote:
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<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@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | (410)
706-7441
==============================**====================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
* Please search the archive at http://www.gromacs.org/**
Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before
posting!
* Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read
http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
--
==================================================
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
==================================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
