Re: [AMBER] How to have a certain number of water molecules?

From: Azade Yazdan Yar <>
Date: Fri, 13 Jan 2017 11:57:49 +0100


Thanks David for your helpful answer. I still have some problem getting
what I want and I think it is because there are steps which I should do but
I am simply not aware of them. Can anyone please help me with this problem:

-I have two residues and for both of them I have the following files:
-using packmol, I put these two residues in a certain number of water
molecules in a box and I get a file: mixture.pdb (which needs editing to be
xleap/antechamber ready)

the problem now is how to get prmtop/inpcrd files from mixtures.pdb in

in case I load the mol2/frcmod files which I had for separate residues, my
guess (and raw try) tells me that xleap does not relate them to mixture.pdb
should I do something here or should I use antechamber on mixture.pdb to
get the mol2 file and then use it in xleap? Is it ok to use antechamber on
solvated residues?

To sum up, my problem is that I have a pdb but I cannot tell xleap where to
get the mol2/frcmod parametres for it. Please let me know if you need any
extra info.

Best regards,

On Tue, Dec 20, 2016 at 7:15 PM, David Case <>

> On Tue, Dec 20, 2016, Azade Yazdan Yar wrote:
> >
> > I am trying to build several boxes which contain different residues. I
> > would like to have the same number of water molecules in all boxes.
> > Is there any easy way to do this? (the 'solvatebox' command is not very
> > number-orientated)
> You can use Amber's AddToBox program, or "packmol". I think both will do
> what
> you want.
> >
> > And my second question is: Imagine I have used the 'solvatebox' command
> on
> > my residue. Is there any way to now undo this? e.g. remove the added
> water
> > molecules from the box?
> ParmEd can do this.
> ...dac
> _______________________________________________
> AMBER mailing list

*A. Yazdan Yar*
*PhD student in Materials Science & Engineering*
*École Polytechnique Federale De Lausanne*
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Received on Fri Jan 13 2017 - 03:00:02 PST
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