RE: AMBER: 31 integers in the first section of a prmtop file

From: David Cerutti <>
Date: Wed, 3 Oct 2007 11:47:42 -0700 (PDT)

Thanks for the clarification, Carlos and Ross.

I'm actually working on a "quality control" code that will automate a lot
of the things I do to make sure that I haven't made mistakes in my
simulation setup or MD input file. It will read and parse a topology,
read a set of coordinates, and then tell you if things look all right. It
should be easily expandable to include other checks, and the stuff I plan
to include should run in about a minute.

Currently, the diagnostics I plan are:

- Check to see that the water (if water is in the simulation) is normal
and alert the user if it's not (SPC/E charges on TIP3P water, for
- Check for possible missing disulfide bridges.
- Check for vacuum bubbles (very useful if running NVT simulations) and
report any such voids in a PDB-format file.
- Create a human-readable description of every distinct residue type to
help users see the residues from a different perspective and thereby
ensure that AMBER understood what they meant if they've introduced
something new.

In the future, we might want to include diagnostics for:

- Minimum distance between two solute images
- The net force on each atom due to particular, nearby solute images

I'm open to other suggestions as I write this code for myself. I expect
that it will save me time and improve my simulations in the long run.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Oct 07 2007 - 06:07:11 PDT
Custom Search