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

Share files, take polls, and make new friends - all under one roof. Click here. ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber@scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo@scripps.edu