Date: Fri, 13 Jul 2001 14:51:42 -0700 (PDT)
From: Thomas Cheatham
Subject: Re: ewald bomb in amber 6


> "Todd J. Minehardt" writes:
> >hi folks.....set up a simulation just as i always do, nothing fancy.....when i try to minimize it,
> >i get the following message:
> >
> >the first lines in min.out are
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 1 nan nan 3.3290E+10 CZ 11209
> >
> > VDWAALS = ************* EEL = nan HBOND = 0.0000
>
> You have atom overlaps (vdw and EEL are huge, bonded terms are reasonable).


An new feature in the latest version of ptraj-- just updated today
at http://www.chpc.utah.edu/~cheatham/software.html-- is the
"checkoverlap" command... This will look for overlaps.

checkoverlap [mask] [min <value>] [max <value>] [noimage]

Search through the selected atoms (all by default) for pair distances
less than the specified minimum value (in angstroms, 1.0 by default) or
greater than the maximum value (if specified). It is a little
computationally demanding since it looks at all pair distances and
images (unless imaging is turned off with the noimage keyword)

For example,

ptraj << EOF
trajin inpcrd
checkoverlap
go
EOF

...will read in the file named "inpcrd" and look for distances between any
pair of atoms < 0.95 angstrom and print out which atoms this is... Very
useful for debugging inpcrd's to look for overlaps.


Also, with respect to the earlier question regarding overlapped ions
placed by LEaP, this is a bug known to the developer's but it hasn't been
tracked down as of yet. If you encounter such a problem, as I did, I was
able to circumvent it by adding the ions 1 ion at a time,

addions xx NO3- 1
addions xx NO3- 1
addions xx NO3- 1
...