AMBER Archive (2008)

Subject: AMBER: solvent box again

From: iccy liu (
Date: Tue Dec 16 2008 - 12:32:32 CST

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 procedure
> > to do it. Can anyone help me? Since my solvent is a new type of molecule,
> > 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 and
> > loaded it later. what kind of files is needed and how to load the new type
> > 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 use
> that. Just Google for "packmol".
> ...dac
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