AMBER Archive (2008)

Subject: AMBER: setbox for solvateoct model

From: Wang, Xuelin (Xuelin.Wang_at_stjude.org)
Date: Fri Feb 15 2008 - 09:22:07 CST

Dear amber users,

I am trying to mutant an amino acid after equilibration of wide-type protein in TIP3PBOX water box.

The procedure is:

 1. I made a pdb file from rst and top files of WT protein.
 2. I did mutation and reload the new pdb to xleap to generate new top and crd file.
 3. then I run a restrained MD to relax the mutant residue by freezing other residues.

I realized that I have to add box information in step 3. How could I do it since I used solvateoct command to generate water box.
The last line of rst file is:
 70.8274482 70.8274482 70.8274482 109.4712190 109.4712190 109.4712190

Thanks
Xuelin

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