AMBER Archive (2008)

Subject: AMBER: How to add radius of an atom

From: saurabh agrawal (
Date: Mon Apr 21 2008 - 00:45:43 CDT

Dear Amber Users,

The molecule I am using for simulation contains two Selenium atoms (viz. Se1 and Se2). For setting “Se” as an atom type I have used following commands:


>addAtomTypes { {"Se1" "Se" "sp2"} }

addAtomTypes: type Se1 - max length is 2

> addAtomTypes { {"Se2" "Se" "sp2"} }

addAtomTypes: type Se2 - max length is 2


Than to set partial charges for the atom which I have these commands:

> s1=createAtom Se1 Se 0.37744
> s2=createAtom Se2 Se 0.32396

and to set element following commands
> set s1 element Se
> set s2 element Se
My questions are-

1. Is this a correct way to add an atom?

2. How to set atomic radius for Se atom? Because when I add solvent in the system It is giving following output:

> 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.

3.What is the correct value for Se radius?

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