[gmx-users] topology and parameter set up
Jennifer Vo
quyviolet at gmail.com
Mon Feb 2 14:20:53 CET 2015
Dear Justin,
Many thanks for your help. My em.mdp is
integrator = steep
emtol = 100.0
emstep = 0.01
nsteps = 100000
coulombtype = PME
pbc = xyz
My nvt.mdp is
title = Protein-ligand complex NVT equilibration
define = -DPOSRES -DPOSRES_LIG ; position restrain the protein and
ligand
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 500 ; save coordinates every 1.0 ps
nstvout = 500 ; save velocities every 1.0 ps
nstenergy = 500 ; save energies every 1.0 ps
nstlog = 500 ; update log file every 1.0 ps
energygrps = Protein NPD
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = hbonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet
rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)
rvdw = 1.4 ; 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
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein_NPD Water_and_ions ; two coupling groups - more
accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one
for each group, in K
; Pressure coupling
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
It generated no error in the log file. This is em.log
Steepest Descents converged to Fmax < 100 in 10536 steps
Potential Energy = -2.1753502e+06
Maximum force = 8.4056786e+01 on atom 100002
Norm of force = 4.0102091e+00
For the NPT.mdp, since I have got error from the previous run, so I tried
commenting out the neighborsearching part to take the default number and
there is still error as the previous email.
Regarding the coordinates, I merged 2 coordinate files into 1 file as your
tutorial about Protein-Ligand Simulation (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html)
and
run a genconf to renumber the system, editconf to create the cubic box and
genbox to solvate the system. Then I add 24 NA since the charge of the
whole system is -24.
I don't know which step is a possible cause to the error.
Regards,
Jennifer
On Mon, Feb 2, 2015 at 1:57 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 2/2/15 6:37 AM, Jennifer Vo wrote:
>
>> Dear Experts,
>> I am facing the problem of simulation of protein - ligand complex using
>> amber99sb force field.
>> Since I created a topol.top for the system
>>
>> ; Include forcefield parameters
>> #include "amber99sb.ff/forcefield.itp"
>> [ atomtypes ]
>> ;name bond_type mass charge ptype sigma epsilon
>> Amb
>> CA CA 0.00000 0.00000 A 3.39967e-01 3.59824e-01
>> ;
>> 1.91 0.0860
>> H4 H4 0.00000 0.00000 A 2.51055e-01 6.27600e-02
>> ;
>> 1.41 0.0150
>> HA HA 0.00000 0.00000 A 2.59964e-01 6.27600e-02
>> ;
>> 1.46 0.0150
>> C C 0.00000 0.00000 A 3.39967e-01 3.59824e-01
>> ;
>> 1.91 0.0860
>> O O 0.00000 0.00000 A 2.95992e-01 8.78640e-01
>> ;
>> 1.66 0.2100
>> N N 0.00000 0.00000 A 3.25000e-01 7.11280e-01
>> ;
>> 1.82 0.1700
>> H H 0.00000 0.00000 A 1.06908e-01 6.56888e-02
>> ;
>> 0.60 0.0157
>> N* N* 0.00000 0.00000 A 3.25000e-01 7.11280e-01
>> ;
>> 1.82 0.1700
>> CT CT 0.00000 0.00000 A 3.39967e-01 4.57730e-01
>> ;
>> 1.91 0.1094
>> H2 H2 0.00000 0.00000 A 2.29317e-01 6.56888e-02
>> ;
>> 1.29 0.0157
>> H1 H1 0.00000 0.00000 A 2.47135e-01 6.56888e-02
>> ;
>> 1.39 0.0157
>> OH OH 0.00000 0.00000 A 3.06647e-01 8.80314e-01
>> ;
>> 1.72 0.2104
>> HO HO 0.00000 0.00000 A 0.00000e+00 0.00000e+00
>> ;
>> 0.00 0.0000
>> OS OS 0.00000 0.00000 A 3.00001e-01 7.11280e-01
>> ;
>> 1.68 0.1700
>> P P 0.00000 0.00000 A 3.74177e-01 8.36800e-01
>> ;
>> 2.10 0.2000
>> O2 O2 0.00000 0.00000 A 2.95992e-01 8.78640e-01
>> ;
>> 1.66 0.2100
>> CK CK 0.00000 0.00000 A 3.39967e-01 3.59824e-01
>> ;
>> 1.91 0.0860
>> H5 H5 0.00000 0.00000 A 2.42146e-01 6.27600e-02
>> ;
>> 1.36 0.0150
>> NB NB 0.00000 0.00000 A 3.25000e-01 7.11280e-01
>> ;
>> 1.82 0.1700
>> CB CB 0.00000 0.00000 A 3.39967e-01 3.59824e-01
>> ;
>> 1.91 0.0860
>> N2 N2 0.00000 0.00000 A 3.25000e-01 7.11280e-01
>> ;
>> 1.82 0.1700
>> NC NC 0.00000 0.00000 A 3.25000e-01 7.11280e-01
>> ;
>> 1.82 0.1700
>> CQ CQ 0.00000 0.00000 A 3.39967e-01 3.59824e-01
>> ;
>> 1.91 0.0860
>> ; Include chain topologies
>> #include "A.itp"
>> ; Include Position restraint file
>> #ifdef POSRES
>> #include "posre_A.itp"
>> #endif
>> ; Include chain topologies
>> #include "B.itp"
>> ; Include Position restraint file
>> #ifdef POSRES
>> #include "posre_B.itp"
>> #endif
>> ; Include custom ligand topologies
>> #include "npd.itp"
>> ; Ligand position restraints
>> #ifdef POSRES_LIG
>> #include "posre_npd.itp"
>> #endif
>>
>> ; Include water topology
>> #include "amber99sb.ff/tip3p.itp"
>>
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ; i funct fcx fcy fcz
>> 1 1 1000 1000 1000
>> #endif
>> ; Include generic ion topology
>> #include "amber99sb.ff/ions.itp"
>>
>> [ system ]
>> ; Name
>> system in water
>> [ molecules ]
>> ; Compound #mols
>> A 1
>> B 1
>> NPD 1
>> SOL 42322
>> NA 24
>>
>> The Protein and the Ligand were under energy minimization and a short MD
>> separatedly to be sure there is no problem with the topology. But when I
>> merge two topol.top from protein and from ligand, the error came at NPT
>> step after successfully energy minimization and NVT
>> "This is likely either a 1,4 interaction, or a listed interaction inside a
>> smaller molecule you are decoupling during a free energy calculation.
>> Since
>> interactions at distances beyond the table cannot be computed, they are
>> skipped until they are inside the table limit again. You will only see
>> this
>> message once, even if it occurs for several interactions.
>> IMPORTANT: This should not happen in a stable simulation, so there is
>> probably something wrong with your system. Only change the table-extension
>> distance in the mdp file if you are really sure that is the reason."
>>
>> This is NPT.mdp
>> title = system in water
>> define = -DPOSRES -DPOSRES_LIG ; position restrain the protein
>> ; Run parameters
>> integrator = md ; leap-frog integrator
>> nsteps = 500000 ; 2 * 500000 = 1000 ps, 1 ns
>> dt = 0.002 ; 2 fs
>> ; Output control
>> nstxout = 5000 ; save coordinates every 1.0 ps
>> nstvout = 5000 ; save velocities every 1.0 ps
>> nstenergy = 500 ; save energies every 1.0 ps
>> nstlog = 500 ; update log file every 1.0 ps
>> energygrps = Protein NPD
>> ; Bond parameters
>> continuation = yes ; Restarting after NVT
>> 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
>>
>> ; Neighborsearching
>> ;ns_type = grid ; search neighboring grid cels
>> ;nstlist = 5 ; 10 fs
>> ;rlist = 1.4 ; short-range neighborlist cutoff (in nm)
>> ;rcoulomb = 1.4 ; short-range electrostatic cutoff (in
>> nm)
>> ;rvdw = 1.4 ; short-range van der Waals cutoff (in
>> nm)
>>
>>
> You have commented out the most critical elements of the input file. You
> need to specify your nonbonded settings, otherwise you're relying solely on
> defaults, which may or may not be right for the force field you're using.
>
>
> ; 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 = V-rescale ; modified Berendsen
>> thermostat
>> tc-grps = Protein_NPD Water_and_ions ; two coupling groups -
>> more accurate
>> tau_t = 0.1 0.1 ; time constant, in ps
>> ref_t = 300 300 ; reference temperature, one for
>> each group, in K
>> ; Pressure coupling is on
>> pcoupl = Berendsen ; Pressure coupling on in NPT
>> pcoupltype = isotropic ; uniform scaling of
>> box vectors
>> tau_p = 2.0 ; time constant, in ps
>> ref_p = 1.0 ; reference pressure,
>> in bar
>> compressibility = 4.5e-5 ; isothermal compressibility
>> of
>> water, bar^-1
>> refcoord_scaling = com
>> ; 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
>>
>>
> Given that you're not generating velocities, presumably you're picking up
> from a previous run? What were its settings and ensemble? Was it stable?
>
> Also be sure to check the merged coordinates and make sure energy
> minimization was sensible.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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