Hi everyone,
In late June, a commit mistakenly replaced NA parameters with those for the sodium ion when using the TIP3P monovalent ion parameters. As the NA atom type is common in proteins and nucleic acids, it's possible that anyone that created a topology file after June 24th has a handful of nitrogen atoms with a mass of 22.99 and "strange" Lennard-Jones parameters. Because this bug was in an frcmod file rather than source code, it will pop up following any git pull, even if you didn't recompile.
This has been fixed in git as of yesterday, but I wanted to issue a warning to you in case anybody regularly uses the head of master in their everyday work.
There is a pretty simple way to detect if you are affected by this -- just take a look at the masses of your NA atom types. They should be ~14, so if they are ~23 you should remake your topology file and rerun calculations you carried out with them. A quick 1-liner to do this:
bash$ echo "printDetails .%NA" | parmed.py -p <your_prmtop>
That should print out the masses of all NA atom types. Sorry for any inconvenience.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jul 22 2014 - 10:30:02 PDT
