If everything is in Amber you could share the inputs for min and md if you
still have trouble. Also first step of each output.
On Mon, Jul 8, 2019, 1:33 PM Bowman, Jacob <bowman.1334.buckeyemail.osu.edu>
wrote:
> This is an error when using Amber for simulations.
>
>
> The exact error message is:
>
> "ERROR: Atom 13272 velocity is -3401.72 -6060.9 7670.82 (limit is 8000,
> atom 134 of 191 on patch 138 pe 7)"
>
>
> But This error is for nearly all of the EPW "atoms" in the simulation.
>
>
> I'll try the simulation without the ligand as well.
>
>
> Thanks,
>
> Jacob
>
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Monday, July 8, 2019 1:29:40 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] EPW "ATOMS Moving too fast" - TIP4PEW
>
> Can you clarify what you mean by "NAMD with Amber"? Is this a NAMD error,
> or when you use Amber for simulations?
>
> I would also see if the problem occurs without the ligand; often errors can
> be a sign of issues with user defined force field parameters.
>
> On Mon, Jul 8, 2019, 1:25 PM Bowman, Jacob <
> bowman.1334.buckeyemail.osu.edu>
> wrote:
>
> > Hello Amber Users,
> >
> >
> > I am currently using NAMD with Amber to run a simulation of a
> > protein/ligand complex in an octahedral water box with TIP4Pew water
> model.
> >
> >
> > The initial structure comes from the end of a previous simulation that is
> > provided by a tutorial for the program SEEKR. TLEAP is used with this
> file:
> >
> > "source /path/.conda/envs/conda_seekr5/dat/leap/cmd/leaprc.protein.ff14SB
> > source /path/.conda/envs/conda_seekr5/dat/leap/cmd/leaprc.gaff
> > source /path/.conda/envs/conda_seekr5/dat/leap/cmd/leaprc.water.tip4pew
> > set default FlexibleWater on
> > set default PBRadii mbondi2
> > loadoff /path/SEEKR/Tutorial/Ca2.lib
> > loadoff /path/SEEKR/Tutorial/benzamidine.lib
> > loadamberparams /path/SEEKR/Tutorial/benzamidine.frcmod
> > WAT= T4E
> > HOH= T4E
> > loadAmberParams
> > /path/.conda/envs/conda_seekr5/dat/leap/parm/frcmod.ionsjc_tip4pew
> > loadAmberParams
> /path/.conda/envs/conda_seekr5/dat/leap/parm/frcmod.tip4pew
> >
> > holo = loadpdb
> >
> /path/SEEKR/Tutorial/root_dir/anchor_2_2_site1_-1.1_19.6_18.3_0/md/holo_wet.pdb
> >
> > bond holo.7.SG holo.137.SG
> > bond holo.25.SG holo.41.SG
> > bond holo.109.SG holo.210.SG
> > bond holo.116.SG holo.183.SG
> > bond holo.148.SG holo.162.SG
> > bond holo.173.SG holo.197.SG
> > charge holo
> > check holo
> >
> > saveamberparm holo
> >
> /path/SEEKR/Tutorial/root_dir/anchor_2_2_site1_-1.1_19.6_18.3_0/md/building/holo2.parm7
> >
> /path/SEEKR/Tutorial/root_dir/anchor_2_2_site1_-1.1_19.6_18.3_0/md/building/holo2.rst7
> >
> > savepdb holo /path/holo_leap.pdb
> >
> > quit
> > "
> >
> > I get the note:
> >
> > Note: 1-4: angle 23026 23027 duplicates bond ('triangular' bond) or angle
> > ('square' bond)
> > For nearly all the water molecules.
> >
> > Then I am able to run a minimization for the water molecules with the
> > protein/ligand atoms fixed.
> >
> > When I move on to a temperature equilibration stage, I run into the
> error:
> > Atoms moving too fast - and they are all exclusively the EPW atoms. I
> have
> > run the minimization for longer and tried to reduce the temperature on
> the
> > temperature equilibration to no avail. Is there any way to overcome this
> > issue? I have tried this same scheme with the TIP3P model and it works
> just
> > fine. I'm not sure where the error with the TIP4Pew is coming from.
> >
> >
> >
> > Jacob Bowman
> >
> > OSBP Graduate Student
> >
> > Lindert Lab
> >
> > Department of Chemistry and Biochemistry
> >
> > 2116 Newman Wolfrom
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Mon Jul 08 2019 - 12:00:02 PDT
