Thanks a lot for your replies. Well, the same error msg appears even
if I have deleted Mg-ATP from the pdb. As suggested, I looked at my
initial pdb structure,
ATOM 919 CG1 VAL A 126 15.020 10.602 2.155 1.00 40.87 C
ATOM 920 CG2 VAL A 126 14.615 12.941 2.762 1.00 43.82 C
ATOM 921 N GLY A 128 17.832 10.976 0.712 1.00 52.78 N
ATOM 922 CA GLY A 128 18.873 10.542 -0.212 1.00 59.95 C
However, I found that after 126 it is 128, but this sequence has been
corrected in 'tleap' as:
ATOM 1831 C VAL 126 36.583 33.672 43.611
ATOM 1832 O VAL 126 37.744 33.723 44.012
ATOM 1833 N GLY 127 36.305 33.201 42.383
ATOM 1834 H GLY 127 35.343 33.143 42.082
Is this the problem?
Surprisingly, the highest energy is seen at
ATOM 2239 3HE MET 154 48.483 34.334 23.516
This residue is MET 155 at the original starting PDB structure.
And I looked at this position and did not find any overlapped atoms.
Could you kindly suggest me as how to fix this?
Thanks again.
Devrani
N.B. Accidentally I pressed the 'send' button before sending this
mail, please ignore that blank msg.
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
