AMBER Archive (2006)

Subject: Re: AMBER: how to add hydrogen molecules in the protein

From: David A. Case (
Date: Thu Oct 26 2006 - 19:57:22 CDT

On Thu, Oct 26, 2006, Rachel wrote:
> Now I have another question, I want to add a few hydrogen molecules into my
> protein, I want to use the hydrogen model of Hunter et al., which is a three
> point molecule with two atoms and a dummy placed at their midpoint, and the
> charges for the two hydrogen atoms are 0.475 while it is -0.95 for the
> dummy. Anyone can tell me how to do that? also if I want to add for example
> 100 hydrogen molecules, do i need to use the add command for 100 times?

Basically, you need to create a mol2 file (easiest format) that has
coordinates and charges for a single hydogen moleucle. You also need to
create a frcmod file that contains other force field parameters (bond length,
force constants, van der Waals parameters....). [LEaP will let you know if
you miss something that is needed, then you can add it in.]

If you know where the hydrogens should be placed, then put those coordinates
in a pdb file along with the protein. Put a "TER" card in between each
hydrogen molecule, so LEaP will know not to try to create a bond between them.

I'm sure I am forgetting something, but don't be afraid to experiment. The
program generally gives reasonable error messages (once you get the hang of
it) if there is something it doesn't like. And you may have to be both
patient and inventive, since dissolving a protein in hydrogen is not all that
common a task....

...good luck...dac

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