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

From: Siddharth Rastogi <>
Date: Mon, 13 Oct 2008 21:34:58 -0700

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.


Siddharth Rastogi

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Received on Wed Oct 15 2008 - 05:09:15 PDT
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