AMBER Archive (2008)

Subject: RE: AMBER: solvent box again

From: iccy liu (
Date: Thu Dec 18 2008 - 13:41:41 CST

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:
source leaprc.ff03
source leaprc.gaff

loadamberprep emi.prepin
loadamberparams emi.frcmod
loadamberprep ACETATE.prepin
loadamberparams ACETATE.frcmod

emacbox = loadpdb EMAC24A_new.pdb

setBox emacbox vdw

saveamberparm emacbox emacbox_new.prmtop emacbox_new.inpcrd
to create topology file and input coordinate

Later I run min and heat in NVT ensemble to relax the system, here is my last heat4.inp
  imin=0, irest=1, ntx=5,
  nstlim=10000, dt=0.001,
  ntc=2, ntf=2,
  ntt=1, tautp=1.0,
  tempi=100.0, temp0=300.0,
  ntpr=50, ntwx=50,
  ntb=0, igb=0,
after running sander with command:
sander -O -i heat4.inp -o heat4.out -c heat3.rst \
                    -p emacbox_new.prmtop \
                    -r heat4.rst -x heat4.mdcrd
I obtained heat4.rst file.

I restart my simulation to run npt_relax.inp
relax at Constant Pressure at 300K
  imin=0, irest=1, ntx=7,
  nstlim=100000, dt=0.001,
  ntb=2, PRES0=1.0, ntp=1, taup=2.0,
  ntc=2, ntf=2,
  tempi=300.0, temp0=300.0,
  ntt=3, gamma_ln = 1.0,
  ntpr=50, ntwx=50,
with command:
sander -O -i npt_relax.inp -o test.out -c heat4.rst \

                    -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.


Subject: RE: AMBER: solvent box again
Date: Tue, 16 Dec 2008 10:57:01 -0800

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

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


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