So in the vacuum when you get this error, what is happening in the
trajectory? Some atom must be zooming off to somewhere, is it the Mg? Why
is it that you don't want to just have the ATP as a residue and then your
modified Mg parameters used to make the Mg residue? The way it seems now
you have a residue that isn't actually all covalently linked, that seems a
bit strange.
~Aron
On Tue, Dec 13, 2011 at 11:43 AM, Xiaozhou Li <xli12.qub.ac.uk> wrote:
> Hi Farid and Aron,
>
> Thanks a lot for your advice.
>
> The method of raising temperature which Farid mentioned didn't make sense,
> with the same issue.
>
> Following Aron's advice, I took the simulation in a vacuum (ntb=0) just
> now, yet the "vlimit exceeded" warning came out again.
>
> What I've modified from my previous work (mentioned at the last of my
> first post) was to treat magnesium ion as a part of ATP, i.e. share the
> same residue name and residue number in PDB file. The "vlimit exceeded"
> warning has never appeared in the previous work as I utilized the "MG2"
> template which was a AMBER built-in residue.
>
> I'm wondering is it an issue which has relationship to bond/angle/dihedral
> parameters which should be given (but not given in my case) in ".frcmod"
> file. Refer to the tutorial file (
> http://ambermd.org/tutorials/advanced/tutorial1_adv/), it gave out those
> information and said "Creating a set of parameters is a bit of an art,
> since one is often faced with unknown parameters (such as force constants
> for copper to its ligands as in this example). So I provide you all of the
> parameters below".
>
> Does anyone know that is it necessary (or even compulsory) to define those
> bond/angle/dihedral and nonbon parameters, to avoid warnings like "vlimit
> exceeded"?
>
> ________________________________________
> From: Aron Broom [broomsday.gmail.com]
> Sent: 13 December 2011 15:56
> To: AMBER Mailing List
> Subject: Re: [AMBER] vlimit exceeded issue
>
> Are you able to determine which atom actually had the velocity limit
> issue? I'm assuming it was the magnesium, but maybe that isn't true.
> Also, I assume from what you've written that this is in water with
> counterions and your protein. Did you try just the ATP + Mg in a vacuum
> first? It might be helpful to start there, and then move to just the ATP +
> Mg in a small box of water, and then finally integrate the whole system.
>
> One other note, as was brought up by Brian, is there a particular reason
> that you are choosing NVE ensemble rather than NTP?
>
> ~Aron
>
> On Tue, Dec 13, 2011 at 10:41 AM, Xiaozhou Li <xli12.qub.ac.uk> wrote:
>
> > Hi Brian,
> >
> > Many thanks for your reply. I'll following the point you've raised to
> make
> > a discussion below.
> >
> > 1) Well, exactly. Magnesium parameters varies a lot depending on the
> > system we considering. I've looked up some literatures to see whether
> > similar system existed as it wasn't a brand-new coordinating environment.
> > Several groups of data were obtained but none of them was suitable for my
> > system. Anyway this review-and-try work is still on processing.
> >
> > 2) For a macromolecule system, 5000 steps of minimization is relatively a
> > common one. Actually I've tried 1000 steps of minimization but still
> failed.
> >
> > 3) Enzymes usually works on a proper temperature (for example, body
> > temperature), and that is why I should make the heating step-- make the
> > simulation more reliable. There's no velocity data obtained from
> > minimization step. Other trials with tempi=10, =20, =30 were conducted
> > and... all failed with the same problem (vlimit exceeded). Plus, the
> > reference temperature could not be ignored as another trial mentioned at
> > the last of my first post, everything went fine when utilizing the same
> > simulation conditions in MD step.
> >
> > Starting with a desired temperature for a large system doesn't work and
> > the reason is just what you said.
> >
> > Thanks in advance,
> > Xiaozhou
> > ________________________________________
> > From: Brian Radak [radak004.umn.edu]
> > Sent: 13 December 2011 15:04
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] vlimit exceeded issue
> >
> > A few things that may hopefully address your problems:
> >
> > 1.) Magnesium parameters are generally considered to be highly
> application
> > dependent. I don't think anyone in the AMBER community has advocated a
> > single "best" set yet. You probably want to carefully search the
> > literature and run some basic tests before settling on a model. It
> > probably won't be one that is released with AMBER (i.e. is already in a
> > parm or frcmod file).
> >
> > 2.) In my opinion, and others here might agree, 5000 steps of
> minimization
> > is rather extraneous and probably more likely to cause new problems than
> > resolve old ones. 1000 TOTAL is probably a more useful value.
> >
> > 3.) I'm not sure what you were meaning to do with your heating. As is,
> you
> > are specifying 0 initial temperature (tempi) so that all velocities are
> > zero (probably not good). The reference temperature (temp0) will
> probably
> > be ignored since you specified NVE dynamics (ntt=1), but I don't know for
> > sure.
> >
> > There are many many heating procedures that you could use, but I don't
> know
> > enough to recommend you a specific. For small molecules I've had
> > reasonable success with just starting at the desired temperature, but I
> > think that may fail for larger systems, especially if the initial
> > coordinates are from a low temperature crystal structure.
> >
> > Regards,
> > Brian
> >
> > On Tue, Dec 13, 2011 at 9:23 AM, Xiaozhou Li <xli12.qub.ac.uk> wrote:
> >
> > > Dear AMBER users,
> > >
> > > I'm now working on a MD simulation to an enzyme which has peculiar
> > > ligands. Followed the official tutorial which dealing with non-standard
> > > residue (link: http://ambermd.org/tutorials/advanced/tutorial1_adv/) I
> > > created a new residue "ATP" which contains an ATP as well as a
> magnesium
> > > ion (nominated as "MG" and it does not exist in the library).
> > >
> > > The template of the new residue was first generated by Gaussian 09 (by
> > > single point charge calculation), then use "antechamber" in AMBER to
> > shift
> > > it into ".mol2" format, which contains atom charges and connection
> > > information, etc. A ".frcmod" file was created simultaneously, said
> that
> > > the MASS and NONBON parameters of MG should be revised. MASS was pretty
> > > easy to obtain, NONBON was directly use those original information in
> > AMBER
> > > lib.
> > >
> > > In "tleap", the residue I manually created was imported directly by the
> > > command "loadmol2". The final model for simulation was then
> successfully
> > > generated. The minimization step was OK, using 5000 step of SD method
> as
> > > well as 5000 step of CONJ method without restriction to the protein.
> > Issue
> > > occurred when it came to the starting point of heating step:
> > >
> > > (the last lines in the output file)
> > > vlimit exceeded for step 3; vmax = 21.5763
> > > vlimit exceeded for step 4; vmax = 115.6802
> > > vlimit exceeded for step 5; vmax = 221.8382
> > > vlimit exceeded for step 6; vmax = 74.7778
> > > vlimit exceeded for step 7; vmax = 42.8791
> > >
> > > Here are the ".frcmod" file and my MD input condition:
> > >
> > >
> > >
> > > (.frcmod file)
> > >
> > > ------------------------------------------------
> > > remark goes here
> > > MASS
> > > MG 24.305
> > >
> > > BOND
> > >
> > > ANGLE
> > >
> > > DIHE
> > >
> > > IMPROPER
> > > c3-ca-na-cc 1.1 180.0 2.0 Using
> default
> > > value
> > > h5-na-cc-nd 1.1 180.0 2.0 Using
> default
> > > value
> > > ca-ca-ca-nd 1.1 180.0 2.0 Using
> default
> > > value
> > > ca-nb-ca-nh 1.1 180.0 2.0 Using
> default
> > > value
> > > ca-hn-nh-hn 1.1 180.0 2.0 Using
> default
> > > value
> > > h5-nb-ca-nb 1.1 180.0 2.0 Using
> default
> > > value
> > > ca-na-ca-nb 1.1 180.0 2.0 Using
> default
> > > value
> > >
> > > NONBON
> > > MG 0.7926 0.8947 ATTN, need revision
> > > ------------------------------------------------
> > > (MD input file)
> > > ------------------------------------------------
> > > Heating
> > > &cntrl
> > > imin=0,irest=0,ntx=1,ntb=1,
> > > cut=10.0,ntr=1,restraint_wt=0.5,restraintmask=':1-395',
> > > ntc=2,ntf=2,
> > > tempi=0.0,temp0=300.0,
> > > ntt=1,nstlim=50000,dt=0.001,ntpr=100,ntwx=100,ntwr=200
> > >
> > > I'm pretty appreciated if anyone could help me to get through that
> issue.
> > >
> > > P.S. In my previous work, I utilized the normal template which exist in
> > > the AMBER lib (name: MG2) for the magnesium ion. The template of ATP
> did
> > > not contain the magnesium ion. The ".frcmod" file corresponding to ATP
> > was
> > > just as the one I provided above, but without information on MG.
> > Everything
> > > went fine from minimization to heating, equilibration and MD simulation
> > > with NPT ensemble. Hopefully what I mention here make sense.
> > >
> > > Many thanks,
> > > Xiaozhou
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > ================================ Current Address =======================
> > Brian Radak : BioMaPS
> > Institute for Quantitative Biology
> > PhD candidate - York Research Group : Rutgers, The State
> > University of New Jersey
> > University of Minnesota - Twin Cities : Center for
> Integrative
> > Proteomics Room 308
> > Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> > Department of Chemistry : Piscataway, NJ
> > 08854-8066
> > radak004.umn.edu :
> > radakb.biomaps.rutgers.edu
> > ====================================================================
> > Sorry for the multiple e-mail addresses, just use the institute
> appropriate
> > address.
> > _______________________________________________
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> > AMBER.ambermd.org
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> >
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Received on Tue Dec 13 2011 - 09:30:03 PST
