RE: AMBER: ADDIONS do not neutralize to ZERO

From: Akshay Patny <>
Date: Mon, 29 Jan 2007 11:04:58 -0600

Dear Ross

Thanks a lot for your suggestions.

As you said I do not need to worry about my 0.999960 charge on ligand, which
might be due to rounding issues. I understand that. However, I guess I
overlooked another problem in my ligand charge (which I think requires a
separate thread: I have sent it under: "RE: AMBER: RESP Charges for Charged
Carboxylate in Organic Ligand").

Regarding my charge of 0.970410 in the system, I checked and my system
without ligand, and you are right>>

Total unperturbed charge: 13.9705
Total perturbed charge: 13.9705

So, my system (protein-lipid-water) essentially has a + 13.9705 charge. Now,
I also checked my lipid (DMP) unit for charge, and although it should be
neutral, It has a residual charge of::

> charge DMP
Total unperturbed charge: -0.0002
Total perturbed charge: -0.0002
> check DMP
Checking 'DMP'....
Checking parameters for unit 'DMP'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.

You suggested that it is possible that my system have one less hydrogen, but
I used leap to add hydrogens except for waters. Can you suggest where can I
start to look to avoid this 0.9705 charge peoblem?

Best Regards

-----Original Message-----
From: [] On Behalf Of
Ross Walker
Sent: Sunday, January 28, 2007 10:38 PM
Subject: RE: AMBER: ADDIONS do not neutralize to ZERO

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

addions unit Cl- 5

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,

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

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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Received on Wed Jan 31 2007 - 06:07:23 PST
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