VMD-L Mailing List

From: Vlastimil Zíma (zima_at_karlov.mff.cuni.cz)
Date: Wed Jan 06 2016 - 03:27:41 CST

Hi everybody,

I believe I found several bugs in solvate plugin when I tried to use it
with custom solvent.

 * Custom solvent has to have a segment QQQ otherwise it doesn't work and
it is very hard to find where the problem is.
 * All arguments for custom solvent are required, but than is neither
stated not validated when using command line. This causes errors which are
hard to debug.
 * Solvate plugin is able to generate invalid segnames, longer than 4
chars, if the is really large copies of the solvent.
 * Values for -ks argument are required to be selections, not the names of
the atoms as suggested by the help.

I hope at least some of the issues will be addressed.

Vlastimil