AMBER Archive (2007)

Subject: AMBER: TIP5P questions

From: Prashanth Athri (athriprashanth_at_yahoo.com)
Date: Tue Sep 11 2007 - 16:26:56 CDT

Dear all,
I am having the following question regarding TIP5P usage. I am comparing results of TIP5P and TIP3P water (trying) wrt DNA+ ligand simulation.

When I use the following commands:
1. solvateoct co TIP3PBOX 8.0
2. solvateoct co TP5 8.0

Both models add different number of residues
# (1) Gives the following results:
Scaling up box by a factor of 1.255439 to meet diagonal cut criterion
  Solute vdw bounding box: 26.332 28.427 46.640
  Total bounding box for atom centers: 66.727 66.727 66.727
      (box expansion for 'iso' is 97.7%)
  Solvent unit box: 18.774 18.774 18.774
  Volume: 155327.486 A^3 (oct)
  Total mass 81340.042 amu, Density 0.870 g/cc
  Added 4066 residues.

#(2) Gives the following:
Solvent has no box, so preparing by making box including vdw
(Use 'setBox centers' first if box was pre-equilibrated)
Scaling up box by a factor of 1.255439 to meet diagonal cut criterion
  Solute vdw bounding box: 26.332 28.427 46.640
  Total bounding box for atom centers: 66.727 66.727 66.727
      (box expansion for 'iso' is 97.7%)
  Solvent unit box: 3.708 3.678 3.502
  Volume: 155327.486 A^3 (oct)
  Total mass 54099.850 amu, Density 0.578 g/cc
  Added 2554 residues.

My question is why is there such a huge difference in the number of wter molecules added and the density? 4066 TIP3P waters are added whereas only 2554 TIP5P are added.

Additionally, has any studies been done on the effect of using TIP5P on nucleic acids- please share if you know of any?

Thanks in advance

Best wishes,
Prashanth
.

       
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