Re: [AMBER] vlimit exceeded for step

From: Jason Swails <>
Date: Thu, 18 Mar 2010 12:07:34 -0400


On Thu, Mar 18, 2010 at 10:28 AM, Hyma vathi <> wrote:
> Dear Carlos and Ross,
> Thank you for your reply. Now I successfully minimised the protein but when
> I subjected it to heating again there was error message which Iam posting
> below. I am unable to get the problem. I will very greatful if you could
> help me out with the problem.
> And I have another query also, actually I am dealing with a protein which
> has a cofactor which is creating the problem, I did try to carefully extract
> the cofactor from cocrystal structure and correct the atom and bond types
> and saved it in a mol2 format and submitted to antechamber but everytime
> some error regarding its charges arises . Can you please suggest some
> solution regarding its charges? Thank you in advance.
> Here is the input file:
> heat
> protein
>  &cntrl
> imin=0,irest=0,ntx=1,
> nstlim=25000,dt=0.002,
> ntf=5,

Be careful with this variable. Are you sure this is doing what you
want it to? ntf=5 prevents all angle/bond force calculations as I
understand it from the manual. If you want to use typical SHAKE,
which is implied by your 0.002 timestep above, then you should have
ntf = 2 and ntc = 2. If you successfully minimized, perhaps this will
help fix things? If not, keep eliminating 'bells and whistles' from
your simulation (such as your cofactor like Carlos suggested) until
you get it to work so you can nail down what's causing the problems.
I just point this out because ntf=5 is a rather unusual value for this

Good luck!

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
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Received on Thu Mar 18 2010 - 09:30:04 PDT
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