[AMBER] Periodic Box Size and Charge Determination

From: Aronica, Pietro <pietro.aronica07.imperial.ac.uk>
Date: Wed, 22 Jul 2015 11:31:11 +0000


I have a solvated restart file and its appropriate prmtop. On the last line of the restart, there are the three dimensions of the box (all three equal, because I used solvateoct) and the three angles. I have created a pdb file from the restart and the prmtop using cpptraj (center the protein, then autoimage) and then used this<http://ambermd.org/tutorials/advanced/tutorial16/#Estimate_Periodic_Box_Size> file to calculate the box dimensions. The output is very different from the dimensions given at the bottom of the restart file. My question is, then, how can I calculate the "correct" dimensions from the pdb? What are the necessary calculations? Also, is there a way that does not involve vmd? Somewhat unrelated, is there an amber functionality that outputs a pdb's overall charge? I know there's a leap command, but I tried looking for a command-line version and couldn't find one.

Kind regards


AMBER mailing list
Received on Wed Jul 22 2015 - 05:00:03 PDT
Custom Search