AMBER Archive (2006)

Subject: AMBER: a question about "solvateoct" in AMBER 8

From: Chengwen Chen (chenchengwen_at_gmail.com)
Date: Fri Apr 21 2006 - 01:48:14 CDT

Dear all,

I found out that the box size information listed in XLEAP after add the
solvent is different with that in ".inpcrd" file. Why ? Am I wrong? Which
one should I select to set the A, B, C parameters of PME box in the input
file? Thank you in advanced.

XLEAP information:
> solvateoct a TIP3PBOX 10.0
Scaling up box by a factor of 1.371926 to meet diagonal cut criterion
  Solute vdw bounding box: 34.115 45.712 32.074
  Total bounding box for atom centers: 73.150 73.150 73.150
      (box expansion for 'iso' is 46.1%)
  Solvent unit box: 18.774 18.774 18.774
  Volume: 203847.880 A^3 (oct)
  Total mass 107696.280 amu, Density 0.877 g/cc
  Added 5536 residues.

Last line in ".inpcrd" file:
64.2159170 64.2159170 64.2159170 109.4712190 109.4712190 109.4712190

Best Wishes,
Chengwen

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