Re: [AMBER] Generating an asymmetric box for Steered MD

From: Souvik Dey <>
Date: Fri, 17 Apr 2020 02:03:52 -0500

Hi David,

I think I solved the problem I was having earlier, setting up an asymmetric
box and then filling up it with water using setBox and AddToBox. However,
there seems to be a new problem now. There are no bonds shown in the water
molecule which I believe is due to incorrect tleap usage. My steps were as

1. *set mol box { 275.798000335693357 148.5099928379058813
138.670001983642581 }* to set up the box

2. *AddToBox -c smd_trial_orient.pdb -a tip3p.pdb -na 95000 -o solv.pdb -RW
2.25* to fill it up with water

3. Running the usual tleap scripts to load the 14SB and TIP3P parameters,
loading the system and then generating the topology as specified in Amber
tutorial 13.

I think I am missing something here, probably in the water PDB file that I
load. Can you please suggest something about how to solve this issue?


On Thu, Apr 16, 2020 at 8:12 PM Souvik Dey <> wrote:

> >What I am concerned about is how AddToBox would work. For example, let's
>> >say that I want to create a box of 120Å x 60Å x 60Å. and fill it with
>> tip3p
>> >water molecules. If I now try to set the box dimensions by setting -X/Y/Z
>> >AddToBox shows that the identifier -X is unknown.
> I'm lost here, and would need to know exactly what commands you used.
>> AddToBox requires an input pdb file (the -c flag) that has a CRYST1
>> record giving the box information.
> I used the command
> *$AMBERHOME/AddToBox -c smd_trial_orient.pdb -a tip3p.pdb -na 83000 -o
> solv.pdb -RW 6.0*
> with the hope to add 83000 tip3p water molecules to smd_trial_orient.pdb.
> The top of the PDB files read
> *CRYST1 253.753 136.423 126.598 90.00 90.00 90.00 P 1 1*
> However, only 8505 water molecules are added. Why do you think this might
> be happening?
>> >
>> >1. How should I set up my box dimensions before I fill it up with the
>> >required number of solvent molecules by -na flag?
>> See above: this is done with the input pdb file.
>> >2. How would the program understand that the water I add is tip3p since
>> all
>> >I am providing is a PDB file of a single water molecule with the -a flag?
>> It doesn't know that you have TIP3P water: you will specify that later
>> when you run tleap. All AddToBox does is set up a pdb file, with the
>> expectation that you will use loadPdb in tleap later on to actually
>> build the system
> So, after I generate solv.pdb, do I need to run solvateBox again for this?
> Souvik
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Received on Fri Apr 17 2020 - 00:30:02 PDT
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