AMBER Archive (2006)

Subject: Re: AMBER: puzzles about solvatoct or solvatebox

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Tue Oct 17 2006 - 10:05:08 CDT

> >> I found that the solute is not in the center of oct-box
> >
> >It sounds like there is a bug in solvateoct.
> >
> Is it really a bug or not? in MD simulations, the solute must be placed
> in the center of the (oct)box? or just being completely buried in the
> solvent is OK? if the latter is YES, then I'll just increase the buffer
> to 12 to completely solvate my system with the cost of more 2400 waters.

The water boxes are periodic, so the real question is whether your solute
in a periodic sense is surrounded by solvent. It is difficult to create a
periodic box with the solvateoct or solvatebox command that does not
completely solvate the solute. So, if you see holes or incomplete
solvation, *and* you are looking at the raw coordinates (without further
processing or imaging by ptraj or another program), likely something is
wrong as eluded to by Bill Ross.

There previously was (and may still be) a problem with LEaP on certain
platforms (AMD opteron with PGF90 rings a faint bell) that when the
command was run, many many waters were added (more than expected) and the
resulting box had slabs missing and looked funny/elongated (not completely
solvating the ligand). This would lead to prmtops of > 50,000 atoms for a
system that would normally be much smaller. If this is the case, you may
try LEaP on a different platform to see if alternative behavior results.
I really should try to find this bug/problem again and seek to destroy it.

--tom

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu