AMBER Archive (2004)

Subject: RE: AMBER: LINMIN failure

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Jun 10 2004 - 12:10:08 CDT

Hi Mineyuki

Look in the first cycle of your minimisation:

   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 NAN NAN 6.4067E+04 C 6998

 BOND = 4558117.5311 ANGLE = 1310.8486 DIHED =
3688.2075
 VDWAALS = nan EEL = nan HBOND =
0.0000
 1-4 VDW = 2028.5963 1-4 EEL = 22119.3049 RESTRAINT =
0.0000

Your bond energy is huge and you Van Der Waals and electrostatic energy is
infinite. This indicates that there is something very very wrong with your
starting structure. You most likely have two atoms sitting on top of each
other. I would check you starting structure very carefully. You can convert
it to a pdb for viewing with:

ambpdb -p prmtop <inpcrd >start.pdb

Then view it in something like vmd:

vmd start.pdb

Another problem might be with your restraints, what are you giving for the
reference structure? The same file as your inpcrd?

Take a good look at the structure and if you can't see anything wrong please
post the prmtop and
inpcrd files and the command line you are running.

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Mizuguchi Mineyuki
> Sent: 09 June 2004 19:40
> To: amber_at_scripps.edu
> Subject: AMBER: LINMIN failure
>
> Hello, Amber
>
> I am energy-minimizing the system containing a protein and TIP3 water
> moleclues.
> But something is wrong, and the output file says 'LINMIN FAILURE'.
> Attached files are input and output files. Could someone
> advise and help
> me?
>
> Sincerely,
>
> Mineyuki
>

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