AMBER Archive (2009)

Subject: [AMBER] prmtop

From: Mark M Huntress (markmh_at_bgsu.edu)
Date: Sun May 03 2009 - 18:20:39 CDT

Hi, I am modeling a rhodopsin, and in AMBER tleap, I combined the retinal part with the protein part by using the "combine" command, and then got a prmtop file. I thought the prmtop would include a bond between the head and tail atoms, but no bond was added, so I guess I should go into the prmtop file and add one. But the prmtop file is indecipherable. Is there anything I can read that will explain the prmtop file, and how it is organized, and what all the numbers mean? (Or a better way to make the bond?).
 Thanks,
Mark
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