Thank you very much, all.
On Tue, Feb 15, 2022 at 4:17 PM Vic De Roo <Vic.DeRoo.ugent.be> wrote:
> Hey King Wu,
> I’ve been struggling my fair share aswell on lipids,
> However for this particular error
>
>
> ‘
> rfree: Error decoding variable 4 2 from:
>
> ATOM 1 34438 !
> ‘
>
> I think you should erase the tekst,
>
>
> So just:
>
> Hold lipid fixed
>
> 10.0
>
> RES 1 384
>
> END
>
> END
>
>
>
>
>
> Vic De Roo
> PhD Student
> NMRSTR Group<https://www.ugent.be/we/orgchem/nmr-structure-analysis/en>
> Department of Organic and Macromolecular Chemistry
> Krijgslaan 281, S4-bis, 1st floor
> B-9000 GENT
> Belgium
> +32456123894
>
> Van: King Wu<mailto:lodking407.gmail.com>
> Verzonden: dinsdag 15 februari 2022 23:02
> Aan: AMBER Mailing List<mailto:amber.ambermd.org>
> Onderwerp: Re: [AMBER] MD simulations for POPC membrane
>
> 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?
> >>
> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial16%2Findex.php&data=04%7C01%7CVic.DeRoo%40ugent.be%7C49a65fe57d074e6b93a808d9f0cedd98%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637805593545438265%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=2epO%2BgDOdTc4Z%2FgjN4YMrNOtg7GRDbWj8%2FUCa2au%2BcQ%3D&reserved=0
> >>
> >> 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
> >> > > >
> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=04%7C01%7CVic.DeRoo%40ugent.be%7C49a65fe57d074e6b93a808d9f0cedd98%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637805593545438265%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=XjRZpTCtbcv%2F7jNmbCKWRoALGu3DFWHE%2BBkvwBR%2Fmxc%3D&reserved=0
> >> > > >
> >> > > _______________________________________________
> >> > > AMBER mailing list
> >> > > AMBER.ambermd.org
> >> > >
> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=04%7C01%7CVic.DeRoo%40ugent.be%7C49a65fe57d074e6b93a808d9f0cedd98%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637805593545438265%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=XjRZpTCtbcv%2F7jNmbCKWRoALGu3DFWHE%2BBkvwBR%2Fmxc%3D&reserved=0
> >> > >
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> >
> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=04%7C01%7CVic.DeRoo%40ugent.be%7C49a65fe57d074e6b93a808d9f0cedd98%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637805593545438265%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=XjRZpTCtbcv%2F7jNmbCKWRoALGu3DFWHE%2BBkvwBR%2Fmxc%3D&reserved=0
> >> >
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >>
> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=04%7C01%7CVic.DeRoo%40ugent.be%7C49a65fe57d074e6b93a808d9f0cedd98%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637805593545438265%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=XjRZpTCtbcv%2F7jNmbCKWRoALGu3DFWHE%2BBkvwBR%2Fmxc%3D&reserved=0
> >>
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
>
> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=04%7C01%7CVic.DeRoo%40ugent.be%7C49a65fe57d074e6b93a808d9f0cedd98%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637805593545438265%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=XjRZpTCtbcv%2F7jNmbCKWRoALGu3DFWHE%2BBkvwBR%2Fmxc%3D&reserved=0
>
> _______________________________________________
> 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
Received on Tue Feb 15 2022 - 18:00:02 PST
