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
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|\oss Walker
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> -----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 - 06:07:31 PDT
