AMBER Archive (2007)

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

From: David Cerutti (dcerutti_at_mccammon.ucsd.edu)
Date: Wed Oct 03 2007 - 13:47:42 CDT

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
instance).
- 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.

Dave

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