Hi Jeff, On Feb 26, 2008, at 5:34 PM, Jeff Ellena wrote:
> Is there something other than what I did above that can be tried to > get correct geometry when using addAtoms.py with XplorNIH 2.19? Try changing the random number seed and running again. > Is there any way to get pdb and psf file output from addAtoms.py > with XplorNIH 2.19 instead of an error message even if the geometry > is not correct? I've been bit by this bug, and I wrote the underlying algorithm. On the TCL side, I've changed from throwing an error to printing a message, so that I can get some output, even if it's imperfect. But that's suboptimal behavior as well, since you actually have to look at the output of your scripts to discover that something was wrong. > Is there a way to make the addAtoms.py geometry correction more > robust? If yes, what is the best approach? fixupCovalentGeom applies a bunch of short energy minimization schemes, randomly selected from a little library, until the violations are acceptable or the number of tries exceeds a threshold. To be honest, it's a pleasant surprise that it's as robust as it is. Perhaps a change that would help would be to wrap the whole thing up in a larger loop, restarting from the original coordinates (but a new random seed) if the last iteration got stuck. There are other ways of approaching this problem (running a short dynamics trajectory instead of minimization, or randomly perturbing the starting coordinates before re-minimizing), but this procedure is intended to be as gentle as possible, while obtaining the desired covalent geometry. --JK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20080226/4b52fa81/attachment.html
