AMBER Archive (2008)

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

From: Siddharth Rastogi (siddharthrastogi08_at_gmail.com)
Date: Mon Oct 13 2008 - 23:34:58 CDT

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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