Re: AMBER: large number of solvent molecules were added for protein with 221 AA residues

From: Carlos Simmerling <>
Date: Tue, 14 Oct 2008 06:21:46 -0400

it depends on the shape of your molecule, the buffer size, and the
type of box you used. you didn't tell us any of these, so we just have
to guess. I'd say it could be reasonable but does seem like a lot of

On Tue, Oct 14, 2008 at 12:34 AM, Siddharth Rastogi
<> wrote:
> Dear ALL,
> While I add explicitly solvent molecules to my protein (having 221 AA
> residues) using TIP3PBOX model, I observe large number of solvent molecules
> are added. The new pdb file now contains 62346 atoms and 19882 residues
> (including the ions added for neutralisation). Can this be possible?.or I
> have done mistake somewhereelse?
> Total vdw box size: 125.270 81.695 73.748 angstroms.
> Volume: 754725.902 A^3
> Total mass 379395.440 amu, Density 0.835 g/cc
> Added 19680 residues.
> regards,
> Siddharth Rastogi
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Received on Wed Oct 15 2008 - 05:10:11 PDT
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