AMBER Archive (2008)
Subject: RE: AMBER: solvent box again
From: iccy liu (hbliu92_at_hotmail.com)
Hi, Dr. Walker,
Thank you very much for your input. I tried followed your suggestion to relax my solvent box with NPT restarting from my previous NVT md simulations. However strange things happened. My output file is empty and cpu is running. I wonder did you ever meet this kind problem? Here is the detail of my procedure:
I build a box (roughly a 24A cube) with my solvent molecule (EMAC24A_new.pdb). I only have my solvent molecules in my PDB. My purpose is to relax it to get a nice cube relaxed solvent box. I definetely don't need any other solvent from AMBER.
I use tleap command:
emacbox = loadpdb EMAC24A_new.pdb
setBox emacbox vdw
saveamberparm emacbox emacbox_new.prmtop emacbox_new.inpcrd
Later I run min and heat in NVT ensemble to relax the system, here is my last heat4.inp
I restart my simulation to run npt_relax.inp
-p emacbox_new.prmtop \
I met a problem now. My test.out file is empty but sander is still runing on my machine. what could be the problem? In fact, I met similars problems when I restart from NVT restart file to run NPT calculations for other systems.
I also tried to run a similar npt_relax.inp reading from my original emacbox_new.inpcrd, The program seems to be OK.
Could you please help me with that?
Thanks a lot for your kindness.
Have you worked through some of the tutorials on http://ambermd.org/tutorials/ ? If not
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
My question is now: how to solvate my system with my solvent box? what keyword
> Date: Wed, 10 Dec 2008 18:18:56 -0500
> From: case_at_biomaps.rutgers.edu
> To: amber_at_scripps.edu
> 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".
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