AMBER Archive (2008)Subject: AMBER: How to change default radius assigned to an atom
From: saurabh agrawal (imsam100_at_yahoo.co.in)
Date: Mon Apr 21 2008 - 23:47:14 CDT
Dear Amber Users,
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. Which 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.
Please help me in solving this problem.
saurabh
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