Re: [AMBER] 2 types of Chlorine atom (one charge is -1 and other is -0.8)

From: David A Case <>
Date: Wed, 23 Jan 2019 07:46:10 -0500

On Wed, Jan 23, 2019, Saikat Pal wrote:

>Dear all,I want to perform simulation using 2 types of Chlorine atom (one
>charge is -1 and other is -0.8) together in the same system. What should
>I do   ?

Simplest: build the system with all "ordinary" chloride ions (with
charge of -1). Then use the "change" command in parmed to modify the
charges of the ions you wish to change. (This assumes that you want the
same Lennard-Jones parameters, and just want to change the charge;
otherwise, use the changeLJSingleType command as well.)

More complex, but might help if you need to do this many times:

You'll have to invent a new (2-character) atom type for your modified
chloride. Then modify atomic_ions.lib (in AMBERHOME/dat/leap/lib) to
add your new atom type to the library: use the existing chloride as a
template. You'll need a frcmod file to give your new atom type
Lennard-Jones parameters, and an addAtomTypes record to assign an
element. Look at AMBERHOME/dat/leap/parm/frcmod.ionsjc_xxxx (where xxxx
is your desired water type) as a template for making a frcmod file.

It's not all as simple as it might be, admittedly. But after this
exercise, you will understand much more of the innards of how Amber
stores it's atom type information.


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Received on Wed Jan 23 2019 - 05:00:02 PST
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