AMBER Archive (2009)

Subject: RE: [AMBER] prmtop

From: Ross Walker (
Date: Sun May 03 2009 - 21:18:04 CDT

Hi Mark,

> 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?).

I would seriously advise against trying to add the bond within the prmtop
file. This is almost guaranteed to end in tears. Instead I would go back to
leap and add a line to your setup script that contains.

bond mol1.resid.atomid mol2.resid.atomid

Where the resid's and atomid's match the atoms you want to bond. You will of
course require parameters for these if they don't exist. When you try to
save the prmtop and inpcrd file Leap will let you know if any parameters are

Good luck,

|\oss Walker

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| San Diego Supercomputer Center |
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