you also might want to add checking of HIS residue names,
density of the system (maybe easier than actual bubbles, which
would presumably involve looking at volumes/surfaces?),
check the termini to make sure they are reasonable (charged
or blocked), check chiralities (very important!!), cis/trans peptide
bonds.
carlos
On 10/3/07, David Cerutti <dcerutti.mccammon.ucsd.edu> wrote:
>
> 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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--
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling.gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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Received on Sun Oct 07 2007 - 06:07:11 PDT
