AMBER Archive (2009)

Subject: Re: [AMBER] test charge

From: Jenny Iskrenova (jnova2001_at_gmail.com)
Date: Fri Feb 20 2009 - 14:32:14 CST

Dan,

This is from a fellow physicist :)

You don't need to run antechamber on more than one molecule.
Antechamber gives you a prepin file that you later use to get the
force field parameters using parmchk. You need the force field
parameters or frcmod file in leap where you ultimately generate the
two AMBER input files: inpcrd and prmtop. The force field parameters
are the same whether you have one or two or more identical molecules.
All these steps are to make possible a definition of a new, your own
residue in leap to be recognized by AMBER.

You should add the hydrogen later in leap. You can do it by drawing it
by hand -- if you run the xleap or you can add it in the little script
that you use to run leap:
loadamberparams chain.frcmod
loadamberprep chain.prepin
addions
...

If you need more than one molecule/residue, you can use "copy" and
"translate" in leap to arrange as many as you wish.

You may need to add other ions if need be, e.g. Cl-, to neutralize the
system since AMBER wants a neutral system.

-nc 1 means that the total charge of the chain is +1.

This page helped me a lot, you may also want to look at it:
http://www.molecular.cz/~cwiklik/materials/amb_residues.html

Hope this helps!

Jenny

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