VMD-L Mailing List

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Sat Aug 19 2006 - 23:03:40 CDT

Hi,

On Sat, Aug 19, 2006 at 11:35:55PM -0400, Thomas Caulfield wrote:
> Hi John Stone and VMD-Lers,
>
> I am wondering what the work-around is for the psfgen when I want to
> solvate with more than WT99 for the segname. I am making a very
> large solvated system, and when I did a smaller one of up to WT51, I
> was okay. Perhaps there is a way to change the psfgen name for
> waters to W instead of WT for the segname? Then I could at least go
> up to W999. It seems like the WT# size for number of atoms per
> segname is rather variable too. In my earlier WTs, WT8 or WT17 the
> number of atoms is in the 4500 range, yet with WT50 I am getting over
> 25,000 atoms. If I could just enforce every segname to be that
> large, there would be no problem.

What version of VMD are you running? There's a -s option at least in the
latest version of solvate that does what you want.

Best,
Leo