PS - it seems acceptable to fix printed numbers to make residue charges
add up to 0, but the method should be published with any results, so
others can be aware.
Bill
On 10/5/17 3:56 PM, Bill Ross wrote:
> 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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>
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Received on Thu Oct 05 2017 - 16:30:02 PDT
