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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Received on Tue Dec 13 2011 - 09:00:06 PST
