AMBER: How to change default radius assigned to an atom

Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: saurabh agrawal <imsam100.yahoo.co.in>
Date: Tue, 22 Apr 2008 10:17:14 +0530 (IST)

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 Received on Wed Apr 23 2008 - 06:07:43 PDT