On 5/29/07, Ross Walker <ross.rosswalker.co.uk> wrote:
> Dear Devrani,
>
> Here is the first point from your output file:
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 1.1843E+11 2.4284E+10 5.5481E+12 HE3 2239
>
> BOND = 156.1910 ANGLE = 724.2956 DIHED =
> 2575.2795
> VDWAALS = ************* EEL = -129550.8405 HBOND =
> 0.0000
> 1-4 VDW = 1223.8779 1-4 EEL = 11866.6783 RESTRAINT =
> 0.0000
>
> The *'s mean that the value was too large to fit in the space provided. Thus
> your VDW energy is huge and the maximum force GMAX is an astounding 5.5 x
> 10^12 KCal/Mol/A. This likely comes about due to problems with your starting
> structure. You likely have two or more atoms sitting on top of each other.
> Note during minimization the atom with the largest force at each step is
> printed. Above it is at HE3 with number 2239. I suggest you visualize your
> starting structure and look at the area around atome 2239. Once you have
> identified the problem you will need to fix your input structure and then
> re-run the minimization.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
> > -----Original Message-----
> > From: owner-amber.scripps.edu
> > [mailto:owner-amber.scripps.edu] On Behalf Of devrani mitra
> > Sent: Tuesday, May 29, 2007 14:27
> > To: amber.scripps.edu
> > Subject: Re: AMBER: error in running sander
> >
> > Hello
> >
> > I'm attaching the output file for the details. Hope this
> > simplifies the things.
> >
> > Thanks,
> > Devrani
> >
> > On 5/29/07, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
> > > does your a_min_water.out file have any information in it?
> > >
> > > do the test cases pass?
> > >
> > > you need to give us much more information if you want help.
> > >
> > >
> > > On 5/29/07, devrani mitra <devranimitra.gmail.com> wrote:
> > > > Dear AMBER users,
> > > >
> > > > While running sander (for removing the bad contacts) following the
> > > > tutorials, I'm getting the following error message:
> > > >
> > > > >> sander -O -i a_min.in -p a.parm7 -c a.crd -r a_min.rst -o
> > > > a_min_water.out -ref a.rst
> > > >
> > > > p0_29153: p4_error: interrupt SIGSEGV: 11
> > > >
> > > > I'm not getting as which file do I need to correct.
> > Please suggest.
> > > >
> > > > Thanks!
> > > > Devrani
> > > >
> > > > Devrani Mitra, UC Davis
> > > >
> > >
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> > > >
> > >
> > >
> > >
> > >
> >
>
>
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Received on Wed May 30 2007 - 06:07:33 PDT
