Re: [AMBER] net charge problem of Amber Lipid14 Force Field

From: Bill Ross <ross.cgl.ucsf.edu>
Date: Thu, 5 Oct 2017 15:56:08 -0700

This question may depend on the computer architecture used and the
numerical libs, and ultimately roundoff in truncating numbers to print
may make it impossible to find a general solution, except massaging the
numbers after building the model.

Bill

On 10/5/17 3:03 PM, Xibing He wrote:
> Hi Everyone,
>
>
> I just tried the TUTORIAL A16: An Amber Lipid Force Field Tutorial: Lipid14<http://ambermd.org/tutorials/advanced/tutorial16/index.html>
>
> I used Amber and AmberTools 16.
>
>
> I found that in the final generated files, the total charge of 128 DOPC lipids is not zero, but -0.001024.
>
>
> I tracked the source of this non-zero total charge problem back to the lib file of Lipid14 force field: \$AMBERHOME//dat/leap/lib/lipid14.lib. I wrote a python script to analyze the net charges of residues in this file, and got the following results:
>
> resname = CHL net_charge = -0.000000
> resname = LA net_charge = -0.000002
> resname = MY net_charge = -0.000001
> resname = OL net_charge = -0.000002
> resname = PA net_charge = -0.000003
> resname = PC net_charge = -0.000004
> resname = PE net_charge = 0.000002
>
>
> Therefore, the net charge of a DOPC molecule (two OL + one PC) in Lipid14 force field is: 2*(-0.000002) + (-0.000004) = -0.000008, and the net charge of 128 DOPC is 128*(-0.000008) = -0.001024.
>
>
> I think this is a problem which cannot be neglected. As the number of lipids increase, the absolute value of total charge will increase to a significant amount.
>
>
> My temporary solution is manually modifying \$AMBERHOME//dat/leap/lib/lipid14.lib file to make the net charge of each residue zero. Just wonder what's your solution if you have encountered the same problem.
>
>
> Sincerely,
>
>
> Xibing He
>
>
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Received on Thu Oct 05 2017 - 16:00:03 PDT
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