AMBER Archive (2008)

Subject: RE: AMBER: solvent box again

From: Ross Walker (
Date: Tue Dec 16 2008 - 12:57:01 CST

Hi Iccy,


Have you worked through some of the tutorials on ? If not you probably should, particularly
Tutorial B1 which will answer a number of your questions, in particular
things like the solvent box looking like it defuses into space (needs
reimaging) and how to solvate things plus how to equilibrate the density of
the system with NPT (very important when running explicit solvent sims from
systems built in leap.)


Good luck,



From: [] On Behalf Of
iccy liu
Sent: Tuesday, December 16, 2008 10:33 AM
Subject: AMBER: solvent box again


Thanks Dr. Case. That is very helpful.

I build a box size of 20Ax20Ax20A with my solvent molecule, and then run MD
in NVT ensemble to relax it. I did min and heat it up to 300K step wise.
Later I extracted my final structure, I found out that the shape of my
solvent box is not a cub anymore. I guess it probably OK? Right now I have a
final relaxed strucutre in pdb format. I hope I did the right thing for
relaxation. Please let me know if I did anything wrong in the above
precedure. Thanks a lot.

My question is now: how to solvate my system with my solvent box? what
keyword to use? I am very new to Amber. In fact, I still did not figure out
how to solvate my system with a single molecule as Professor Case mentioned
in his reply. Is there any difference between defining solvent and solvating
my system in AMBER with STARTING my system with a single pdb file including
my solute and solvent coordinates to run in gas phase MD simulations? I
really appreciate your help very much.

Best Regards,

Iccy Liu

> Date: Wed, 10 Dec 2008 18:18:56 -0500
> From:
> To:
> Subject: Re: AMBER: how to add new solvent type in Amber
> On Tue, Dec 09, 2008, iccy liu wrote:
> >
> > I have a question about adding a new solvent type in
> > Amber. I did search the manual and tutorials and couldn't find the
> > to do it. Can anyone help me? Since my solvent is a new type of
> > I followed the tutorial 4 and build a single molecule pdb, then using
> > antechamber to generate single solvent molecule *.prepin and *.frcmod
> > file. What is next step should I do? I would like to build a solvent box
> > loaded it later. what kind of files is needed and how to load the new
> > solvent box? Any input will be high appreciated. Thanks a lot!
> Two approaches: you can just solvate with a single molecule, rather than a
> box. This doesn't create a great starting structure, but it can be good
> enough if you follow this with careful equilibration.
> Or, you can try the packmol program to create a starting structure, then
> that. Just Google for "packmol".
> ...dac
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to


Connect to the next generation of MSN Messenger Get it now!

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)