AMBER Archive (2003)

Subject: Re: leap remove command

From: darden (darden_at_gamera.niehs.nih.gov)
Date: Sun Mar 16 2003 - 15:26:02 CST

I've used a painful trial and error method of changing the solvatebox
parameters in leap to get the right number of waters. Its ugly but I don't
have a better idea.
Tom D
 On Fri, 14 Mar 2003, CUI, Guanglei wrote:

> Dear amber users,
> I'm trying to create a solvated system in leap to match a previously
> created restart file. However, leap added two extra water molecules.
> Is there a way to safely delete them? I tried 'remove' command, but
> the following MD (a free energy perturbation) generated lots of
> vlimit warning. Any suggestions? Thanks in advance.
>
> regards,
>
>