Have you carried out simulations in previously? Lipids can be challenging,
and I usually recommend against trying them until you're already
comfortable with how Amber works and what might go wrong in the inputs.
They way you can learn how equilibration works, and the goals of the
individual steps and restraints. After that it is more reasonable to take
on the extra complexities of lipids.
In this case, the original example you're following may have had a protein
or other residues in addition to the lipids, and the author also wanted to
restrain those. Following that tutorial by actually running it and
analyzing the outputs will help you to see what it is doing, and also
ensure that your Amber setup is working properly before you start to make
changes for your own system. Look at the tutorial system - what could the
author have intended by the 384? Is DOPC_128.pdb what is actually being
simulated? If not, is 128 relevant here?
Also, in one place you mention heat.in but a different name in another
spot. Make sure there are no typos either in the scripts or your email, or
else people will get misled into thinking that is the source of the error.
I would strongly suggest that you actually work through the tutorial and
make sure you u serstand each step and each flag, and analyse the results,
and then try to modify it one step at a time.
On Tue, Feb 15, 2022, 5:00 PM King Wu <lodking407.gmail.com> wrote:
> Hi, Amber,
>
> I followed the AMBER tutorial heat.in with the following setup, but got an
> error message in the output file. I also tried the "RES" flag with 1 771 in
> the GROUP and got the same error (because my POPC residues are from 1 to
> 771, or atoms are from 1 to 34438).
>
> Can somebody tell me how to fix this? The tutorial has RES 1 384, but the
> DOPC_128.pdb has 128 lipids, so I am not sure why here it is set to 1 384.
>
> 5. REFERENCE ATOM COORDINATES
>
>
> default_name
>
> ----- READING GROUP 1; TITLE:
>
> Hold lipid fixed
>
>
> GROUP 1 HAS HARMONIC CONSTRAINTS 10.00000
>
>
> rfree: Error decoding variable 4 2 from:
>
> ATOM 1 34438 !
>
> Lipid POPC heating 100K
>
> &cntrl
>
> imin=0, ! Molecular dynamics
>
> ntx=1, ! Positions read formatted with no initial velocities
>
> irest=0, ! No restart
>
> ntc=2, ! SHAKE on for bonds with hydrogen
>
> ntf=2, ! No force evaluation for bonds with hydrogen
>
> tol=0.0000001, ! SHAKE tolerance
>
> nstlim=2500, ! Number of MD steps
>
> ntt=3, ! Langevin thermostat
>
> gamma_ln=1.0, ! Collision frequency for Langevin thermostat
>
> ntr=1, ! Restrain atoms using a harmonic potential
>
> ! (See the GROUP input below)
>
> ig=-1, ! Random seed for Langevin thermostat
>
> ntpr=100,
>
> ntwr=10000,
>
> ntwx=100, ! Write to trajectory file every ntwx steps
>
> dt=0.002, ! Timestep (ps)
>
> nmropt=1, ! NMR restraints will be read (See TEMP0 control below)
>
> ntb=1,
>
> ntp=0,
>
> cut=12.0,
>
> ioutfm=1, ! Write a binary (netcdf) trajectory
>
> ntxo=2, ! Write binary restart files
>
> /
>
> &wt
>
> type='TEMP0', ! Varies the target temperature TEMP0
>
> istep1=0, ! Initial step
>
> istep2=2500, ! Final step
>
> value1=0.0, ! Initial temp0 (K)
>
> value2=100.0 / ! final temp0 (K)
>
> &wt type='END' / ! End of varying conditions
>
> Hold lipid fixed
>
> 10.0 ! Force constant (kcal/(mol Angstroms^2))
>
> ATOM 1 34438 ! Choose residues
>
> END
>
> END ! End GROUP input
>
>
> My run script is : $AMBERHOME/bin/pmemd.cuda -O -i heat01.in -o
> heat01.out
> -p protein_popc_water.prmtop -c min_all.rst -r heat01.rst -x heat01.mdcrd
> -ref min_all.rst
>
> On Tue, Feb 15, 2022 at 9:41 AM King Wu <lodking407.gmail.com> wrote:
>
> > Yes, I did.
> >
> > I compared my input and this tutorial's input, I did not find any
> > restraint flags for the production run. Therefore I went ahead to run my
> > 100ns simulation.
> >
> > But I noticed that there is "RES" in the Heat up steps, and one step to
> > Hold. Is the Hold step a necessary step before production runs?
> >
> > and thank you, Elvis, for the input. Tutorial uses ntp=2, I will use
> ntp=3
> > to give a try, and at the same time, I will try the "RES" flags in the
> > heat.in and then "hold.in" step.
> >
> > On Tue, Feb 15, 2022 at 9:23 AM Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> >> have you looked at the lipid tutorial?
> >> http://ambermd.org/tutorials/advanced/tutorial16/index.php
> >>
> >> On Tue, Feb 15, 2022 at 11:38 AM King Wu <lodking407.gmail.com> wrote:
> >>
> >> > My simulation system includes a protein and a membrane. I want to
> >> > investigate the dynamics of the protein with the presence of a
> membrane.
> >> >
> >> > I used FF14SB for the protein and LIPID17 for the membrane. During the
> >> > equilibrium step, I first restrained the solute and simulated the
> water
> >> at
> >> > 300K, then I heated up the whole system from low T to reach the RT
> >> without
> >> > restraint. Appropriate Na and Cl ions were added to neutralize the
> >> system.
> >> >
> >> > The equ and production MD runs are in the explicit solvent model.
> >> >
> >> > Please let me know if additional info is needed. I would be happy to
> >> > provide.
> >> >
> >> > Thanks.
> >> >
> >> > On Tue, Feb 15, 2022 at 8:26 AM Carlos Simmerling <
> >> > carlos.simmerling.gmail.com> wrote:
> >> >
> >> > > I think people might be able to offer help if you give a lot more
> >> > > information on exactly what you did, and what happened. For example,
> >> you
> >> > > don't say what force field you used for the lipid, or how you
> >> > equilibrated
> >> > > it, or if water was included, and so on.
> >> > >
> >> > > On Tue, Feb 15, 2022 at 11:21 AM King Wu <lodking407.gmail.com>
> >> wrote:
> >> > >
> >> > > > Hi, Amber,
> >> > > >
> >> > > > I wonder if you received my previous email.
> >> > > >
> >> > > > I simulated a 100 ns simulation for a VMD generated POPC
> membrane. I
> >> > > > started with 120 X 80 A dimension, but got an aggregated/folded
> >> > > > conformation of the membrane after 100ns simulation. Do I miss any
> >> > flags
> >> > > > of restrain in the input for my production run?
> >> > > > Because the screenshots are large in size, I could not attach them
> >> for
> >> > > your
> >> > > > reference.
> >> > > > Below is the input:
> >> > > >
> >> > > > &cntrl
> >> > > > imin = 0,
> >> > > > irest = 1,
> >> > > > ntx = 5,
> >> > > > ioutfm = 1,
> >> > > > nstlim = 10000000,
> >> > > > dt = 0.002,
> >> > > > ntt = 3,
> >> > > > gamma_ln = 2.0,
> >> > > > ig = -1,
> >> > > > tempi = 300.0,
> >> > > > temp0 = 300.0,
> >> > > > ntp = 1,
> >> > > > ntb = 2,
> >> > > > ntc = 2,
> >> > > > ntf = 2,
> >> > > > cut = 12,
> >> > > > ntwr = 500,
> >> > > > ntpr = 500,
> >> > > > ntwx = 500,
> >> > > > ntwe = 500,
> >> > > > iwrap = 1,
> >> > > > ntr = 0,
> >> > > > /
> >> > > > $ewald
> >> > > >
> >> > > >
> >> > > > /
> >> > > > _______________________________________________
> >> > > > AMBER mailing list
> >> > > > AMBER.ambermd.org
> >> > > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > > >
> >> > > _______________________________________________
> >> > > AMBER mailing list
> >> > > AMBER.ambermd.org
> >> > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > >
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> _______________________________________________
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> >>
> >
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Received on Tue Feb 15 2022 - 15:30:02 PST
