I am trying to run the ribosome 30s subunit on gromax 4.5. I chose the AMBER force field since it had the least issues with RNA and that made running pdb2gmx much easier. Everything is fine till I run a md. Below I have attached everything I think is informative. I have run a purely protein md with GROMOS96-43a1 and had no problems, but once I try to run this under AMBER03 it fails with LINCS errors.
energy minimization mdp file:
cpp = /usr/bin/cpp
define = -DFLEX_SPC
constraints = none
integrator = steep
nsteps = 5000
;
; Energy minimizing stuff
;
emtol = 200
emstep = 0.01
nstcomm = 1
ns_type = grid
rlist = 1
rcoulomb = 1.0
rvdw = 1.0
Tcoupl = no
Pcoupl = no
gen_vel = no
Positional restraint mdp file:
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.004 ; ps
nsteps = 2500 ; total ps = dt*nsteps
nstcomm = 1
nstxout = 200 ; output coordinates every ps = dt*nstxout
nstvout = 1000 ; output velocities every ps = dt*nstvout
nstfout = 0
nstenergy = 10
nstlog = 10
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on
Tcoupl = v-rescale
tau_t = 0.1 0.1 0.1 0.1 0.1
tc_grps = protein RNA SOL NA CL
ref_t = 310 310 310 310 310
; Pressure coupling is on
pcoupl = berendsen
pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocities is on at 310K (core body temp)
gen_vel = yes
gen_temp = 310.0
gen_seed = 173529
main molecular dynamics mdp file:
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.004 ; ps
nsteps = 25000 ; total ps = dt*nsteps
nstcomm = 1
nstxout = 200 ; output coordinates every ps = dt*nstxout
nstvout = 1000 ; output velocities every ps = dt*nstvout
nstfout = 0
nstenergy = 10
nstlog = 10
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on
Tcoupl = v-rescale
tau_t = 0.1 0.1 0.1 0.1 0.1
tc_grps = protein RNA SOL NA CL
ref_t = 310 310 310 310 310
; Pressure coupling is on
pcoupl = berendsen
pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocities is on at 310K (core body temp)
gen_vel = yes
gen_temp = 310.0
gen_seed = 173529
And my script for running the whole process:
pdb2gmx -f receptor.pdb -o receptor.gro -p receptor.top
editconf -bt cubic -f receptor.gro -o receptor.gro -c -d 1.5
genbox -cp receptor.gro -cs spc216.gro -o receptor_b4ion.gro -p receptor.top
grompp -f em.mdp -c receptor_b4ion.gro -p receptor.top -o receptor_b4ion.tpr
genion -s receptor_b4ion.tpr -o receptor_b4em.gro -neutral -conc 0.0001 -pname NA -nname CL -g receptor_ion.log -p receptor.top
Here I select the SOL for ions...
grompp -f em.mdp -c receptor_b4em.gro -p receptor.top -o receptor_em.tpr
mdrun -v -s receptor_em.tpr -c "$base"_after_em.gro -g emlog.log
grompp -f pr.mdp -c receptor_after_em.gro -p receptor.top -o receptor_pr.tpr
mdrun -v -s receptor_pr.tpr -o receptor_pr.trr -e pr.edr -c receptor_after_pr.gro -g prlog.log -cpi state_pr.cpt -cpo state_pr.cpt
grompp -f md.mdp -c receptor_after_pr.gro -p receptor.top -o receptor_md.tpr
mdrun -s receptor_md.tpr -o receptor_md.trr -c receptor_after_pr.gro -g md.log -e md.edr -cpi state_md.cpt -cpo state_md.cpt
Where receptor is of course my protein/RNA pdb name
I always make sure that the pdb doesn't give me notes or warnings or errors of course in the pdb2gmx step. Most of the time I minimize to my computers "machine precision."
This is the return I get from the "EM" step:
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 200
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 324 steps,
but did not reach the requested Fmax < 200.
Potential Energy = -1.9868888e+07
Maximum force = 8.7276396e+03 on atom 19080
Norm of force = 3.8592850e+01
I will get this error sometime in the "PR" step of my script:
step 0
Step 11 Warning: pressure scaling more than 1%, mu: 1.03087 1.03087 1.03087
Step 11 Warning: pressure scaling more than 1%, mu: 1.03087 1.03087 1.03087
Step 21 Warning: pressure scaling more than 1%, mu: 0.849053 0.849053 0.849053
Step 21 Warning: pressure scaling more than 1%, mu: 0.849053 0.849053 0.849053
Step 22, time 0.088 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.005723, max 0.026407 (between atoms 6545 and 6542)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
I hope this is enough information (and not to lengthy). Any help would be much appreciated.
TJ Mustard
Email: musta...@onid.orst.edu
Cell: 509-879-4173
>
>
> TJ Mustard wrote:
> >
> > First off I am using gromacs 4.5. I will also post all of my files and
> > errors if they help.
> >
> >
> >
> > If I run a protein in GROMOS96 all my md runs complete succesfully. But
> > if I change to any of the AMBER force fields I get LINCS errors in my
> > positional restraint md run. I have tried using shake, 1 fs step sizes,
> > -heavyh, and many more. Does anyone know what is going on here?
> >
>
> A complete (but not overly lengthy) post will save everyone a lot of time.
> Based on the information you've provided here, I see now way to diagnose the
> problem. The most important information to post would be your .mdp file.
> Certain settings can influence stability. A description of the hardware,
> compilers used, etc. can also be useful.
>
> -Justin
>
> >
> >
> > The reason I want to use AMBER is the fact that I want to run md on the
> > 30s rybosome and amber converts RNA much easier than GROMOS force fields.
> >
> >
> >
> >
> >
> > Thank you in advance,
> >
> >
> >
> > TJ Mustard Email: musta...@onid.orst.edu
> > Cell: 509-879-4173
> >
> >
> >
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> 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
>
-- 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
