AMBER Archive (2008)

Subject: Re: AMBER: NAN errors in Etot, EPtot, EKtot and EELEC

From: Praveena Gopal (
Date: Fri Jun 06 2008 - 01:16:40 CDT

Dear Simmerling,
         Thank you so much for your reply. Actually that peptide is the combination of non-natural and natural amino acids. I have optimized it in Gaussian and then built the crd and top parameters with GAFF and then solvated using ff03 force field.
        I will try with the temperature settings and GB solvation as you have mentioned and get back to you with the results..
    Thank you once again,

  Carlos Simmerling <> wrote:
  try assigning an initial temperature (tempi) other than 0.
maybe 200K or so. I find that setting tempi=0 and then using
temp0=300 causes extremely rapid heating and instability.
also 10 kcal/molA^2 is a very large restraint, not a small one.
probably not the problem here, but I just wanted to mention that.
does the dimer work if you use GB solvation? that might help
to know if it is somehow the solvation or if it is the solute.
anything unusual in the peptide- did you use only standard
force field parameters?

On Thu, Jun 5, 2008 at 8:04 AM, Praveena Gopal wrote:
> Dear Amber Users,
> I'm trying to run 20ps initial MD with dt of 0.002ps for a cyclic
> hexapeptide dimer solvated in water using Amber version 8. I've kept the
> dimer fixed with a small restraint of 10kcal/molA2. The output seems to have
> NAN errors for ETOT, EKTOT, EPTOT amd EELEC values. I've searched in mailing
> lists and found few mails regarding that. But unfortunately could not find a
> solution with what is given. Kindly let me know what could be the reason for
> NAN errors. How could I recover from that?
> I've checked the dimer in xleap which seems to be ok in both isolated and
> solvation forms. I've also tried reducing the restraint on solute and by
> turning off the shake. Now the run continues without any NAN error but with
> vilimt exceeding in every steps. However after few steps the program
> terminates automatically with following messages:
> "Frac coord min, max: -7.13960686514676458E-6, 0.70635552688012537
> The system has extended beyond
> the extent of the virtual box.
> Restarting sander will recalculate
> a new virtual box with 30 Angstroms
> extra on each side, if there is a
> restart file for this configuration.
> SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
> Atom out of bounds. If a restart has been written,
> restarting should resolve the error
> As it shows restart would solve the problem, I've tried restarting the
> program. Though it ran for few steps (with vilimt exceeding in every
> steps), program then aborted with the same messages.
> Herewith I have attached the dt=0.001.out and dt=0.002.out files.
> Kindly suggest an idea to rectify.
> Thanks in advance.
> PraveenaG
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