Re: [AMBER] Copper +1 and membrane with LJ 12-6-4 potential

From: Pengfei Li <>
Date: Sat, 27 Aug 2016 16:48:22 -0400

Hi Stephan,

> On Aug 23, 2016, at 10:37 AM, Stephan Schott <> wrote:
> Hi everyone,
> This is a repost from GitHUB, in case someone has an idea around here (
> I'm
> trying to assemble a system with a membrane protein that has a Cu+1 ion
> interacting with it. I found out about the 12-6-4 implementation on AMBER
> and wanted to try it. First, the copper +1 ion polarizability seems to be
> missing from the lj_1264_pol.dat file. Also there was no info about
> polarizabilities for lipid atoms. Considering that there are already a lot
> of assumptions in the polarizability file, I included the missing values
> comparing them to the values already present in the file, and calculated
> the Cu+ polarizability with GAUSSIAN. Is this a correct approach or I'm
> just plain wrong? Here are the values I included.

Yeah, it is the right way to go.

Can you send me the topology file and the lj_1264_pol.dat file you have (you can send them in an independent mail if you like)? I can help to do a check.

Kind regards,
AMBER mailing list
Received on Sat Aug 27 2016 - 14:00:03 PDT
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