AMBER Archive (2008)

Subject: Re: AMBER: How to change default radius assigned to an atom

From: David A. Case (
Date: Tue Apr 22 2008 - 00:36:16 CDT

On Tue, Apr 22, 2008, saurabh agrawal wrote:

I have added a new atom type (present in ligand) through leap.
But wile using solvateoct command it shows 1.5 Angs. radius for Selenium.
I wish to change to the correct radius. May anyone let me know the way to
change it?

> solvateoct c TIP3PBOX 8
 (using default radius 1.500000 for Se1)
 (using default radius 1.500000 for Se2)
Scaling up box by a factor of 1.159796 to meet diagonal cut criterion
  Solute vdw bounding box: 44..319 22.848 42.645
  Total bounding box for atom centers: 62.876 62.876 62.876
      (box expansion for 'iso' is 56.0%)
  Solvent unit box: 18.774 18.774 18.774
 (using default radius 1.500000 for Se1)
 (using default radius 1.500000 for Se2)
  Volume: 130310.325 A^3 (oct)
  Total mass 66695.892 amu, Density 0.850 g/cc
  Added 3240 residues.

First: please post as plain text, not as html.

Second: are you sure this is really a problem? The radius above is only used
to determine how to position waters around the solute, and you are going to
equilibrate that anyway. So any reasonable value is likely to work.

I hope someone on the list knows that answer, or has the time to look in the
code (you could search for "using default radius" and probably get close to
where things are set.). But I suspect that you might as well just continue
with what you did above.


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