AMBER Archive (2003)

Subject: RE: leap remove command

From: Yong Duan (yduan_at_udel.edu)
Date: Sun Mar 16 2003 - 21:31:12 CST

My approach is even uglier (and I actually have not tried myself). But I
think it may work, albeit a bit complicated. I assume that your purpose
is to solvated a new solute with the same number of water molecules. But
you don't really care the initial coordinates of the water.

1) From the RESTRT file, generate a PDB file (let's say it's called
A.PDB).
2) Generate a PDB file of the (new) solute, including ions. Can be done
in leap. Let's call it B.PDB
3) Append the water in A.PDB to the end of B.PDB and the combined PDB
file is called C.PDB
4) In Leap, read in C.PDB and use "addbox" (?) command with a reasonably
large box size. Generate a topology file, C.TOP and restart file C.CRD.
5) Use B.PDB in Leap and solvate it as you built a fresh new system with
a few more water molecules than what you have in C.TOP. Call this D.TOP
and D.CRD.
6) Remove some extra water molecules from D.CRD and put it in E.CRD (by
simply editing the file).

The C.TOP and E.CRD would be the pair you can use to start a new
simulation. You can also copy the box information from D.TOP to C.TOP.
Here, there should be enough cushion to prevent water molecules from
bumping into either solute or the images of other water molecules.

You should understand that the water in E.CRD has not been equilibriated
yet.

By the way, I typically use trial and error to do this and can often get
down to a similar number of water (+/-2, for instance) but not exactly
the same.

I guess by now you can understand why I said "even uglier". Don't try
this if you have any other options.

yong

-----Original Message-----
From: darden [mailto:darden_at_gamera.niehs.nih.gov]
Sent: Sunday, March 16, 2003 4:26 PM
To: CUI, Guanglei
Cc: amber_at_heimdal.compchem.ucsf.edu
Subject: Re: leap remove command

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,
>
>