# RE: AMBER: ADDIONS do not neutralize to ZERO

From: Ross Walker <ross.rosswalker.co.uk>
Date: Sun, 28 Jan 2007 20:38:25 -0800

Dear Akshay,

> How can I neutralize the charge on my ligand which is not integral (it
> is: 0.999960)? As you mentioned that Leap adds ions with integral
> charge and thus the solute must have integral charge to arrive at 0. I
> guess that is the reason TLEAP is not able to neutralize the decimal
> charge on my ligand.

Minor roundoff is not a problem for simulation. However, it does cause
problems in leap. The simplest solution here is instead of telling leap to
neutralize the solute with a 0 simply specify how many ions you want it to
add. E.g. if the system is +4.999960 then

will add 5 ions giving you a net final charge of -0.000040. Sander will
detect this residual charge and remove it by scaling dividing it up between
all the atoms in this system. For a solvated system such a residual charge
will simply be lost in the noise and you won't have a problem.

> You also commented that "If you don't want to neutralize it with an
> ion, I doubt it's a problem." >> Does this mean that I can simulate my
> GPCR-Ligand-Membrane system using an overall net charge of 0.970410,
> IS THIS ALLOWED, I MEAN, WILL THIS CHARGE NOT CREATE ANY ARTIFACTS
> DURING MD SIMULATION?

The issue here is that this is non physical. You cannot create a system in
the lab with 0.97 excess electrons. This almost certainly comes from
something being wrong with the way you have set your system up. You are
likely missing an atom (probably a hydrogen) somewhere and this is why you
have the non-integral charge. So why there is no reason you can't run this
simulation, the amber force field equations (with exception of QM/MM) have
no restriction on an integral charge. However, as I say you will likely just
uncover a problem with the way you initially built your system so you should
try to track this down. If you some modified residue somewhere then you
should probably refit the charge on this by using RESP.

A difference of 0.03 is too big for sander to simply detect and average out
so you should fix it - by finding out what is wrong with the way you built
your system (NOT simply averaging it over other atoms!!!). Your 0.999960 one
you do not need to correct for the extra 4 ten thousandths of an electon.
This has just come about because of rounding issues.

All the best
Ross

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|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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Received on Wed Jan 31 2007 - 06:07:16 PST
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